There's over 150 mods in the game, which you can apply to over 100 units, so listing every possible mod strategy is frankly impossible.
However, you don't need to know every possible combo, you just need to know how to pick an appropriate combo, and once you do, you'll easily be able to come up with your builds. Don't be afraid to experiment - the best combos aren't always the most obvious.
Some major things to consider:
1. Be sure to choose a unit that supports what you're trying to do in the first place. While you can force a unit into an unusual role, and that's *occasionally* a good idea to trick enemies, usually, you'll want to pick a unit that's already good at what you want to do, and make it even better.
2. Some mods suck on their own, but are great as part of a combo.
3. Some mods APPEAR at first glance to be far better or worse than they actually are.
Cerberus is one of the best-known examples of both of these.
Cerberus by itself: +50% shields, +10% regen, 1 damage reduction
HT by itself: +100% shields
Cerb looks better, right? Here's why it isn't: shield regen is not a fixed value, it's a percentage of the total. On any unit with at least 20% shield regen, HT will give more regen than Cerb, and twice the total shield boost. Even if the unit only has 15% regen, you still come out ahead in overall power, since you'll have far more shields, but only a tiny bit less regen. Sometimes, simple really is better. In this case, the "just add a bucketload of shielding" beats "let's boost a unit defensively in 3 different ways, but not do a good job with any of them".
Here's where the combo comes in. What if you use both?
HT and Cerb comboed: +150% shields, +10% regen (stacked with the already massive boost from boosting the total shielding), -1 damage reduction
Suddenly, that Cerb's looking good again. Of course, you may decide that this combo is simply way too much defense for what you're doing, and that's fine. There's definitely cases where it's an awesome thing to have though.
4. Niche mods often shine on specific units.
Let's look at 2 reduction mods.
Sanctuary Dampening Shield: 2 damage reduction
Porcupine Reactive Armor: 3 damage reduction, but only vs. hits that strike armor
Well, in most cases, you want to avoid taking armor damage in the first place, and if you are forced to take some, Sanc still works. So in any normal situation, Sanc is clearly the better mod.
Now look at the Battle Axe series of meka, however. These don't have shields at all. There's no such thing at a hit that didn't strike armor on a Battle Axe. There's nothing else to strike. This means that for those units, Porcupine is simply a stronger Sanc, with no drawback.
5. A gun cannot have 2 properties. Properties include things like mag, mistarget, and rail. So what happens if you equip gyro ammo on a unit with a mag cannon? Well, the mag cannon is already mag, so it cannot be rail as well. This means gyro ammo will do absolutely nothing on that gun. On the other hand, if you equip both cluster missiles and explosive missiles, these stack fine. Cluster gives the other missile launchers a property (mistarget), but explosive does not, so both can be in play on the same gun.
6. Some units just plain suck out of the box, but are very, VERY mod-friendly. Sometimes it's obvious (the Claymore flat out tells you what to do in its description), while other times, you have to think a bit harder. The mite is a HORRIBLE unit unmodded... but it's actually one of the best simples in the game. We'll explore this when we get to sample mod builds.
7. Check the mod list carefully. You may have forgotten something. The first time I did a base seige with BAIIs, I used Sanc, because I flat out forgot Porc existed. Yeah, brilliant move.
8. Consider damage boost mods carefully - they aren't always worth it. For instance, Armor-Piercing Missiles adds 1 missile damage. Try to come up with a build where putting this on a unit is better than adding another gun, or a different missile mod. Yep... there isn't one. Of course, now that this also anti-missile mods, the mod *can* be useful in certain, rare, pvp situations.
9. Try to think of unconventional uses for mods - it can pay off big. Take Natural Armor Acti - an acti that consumes ore deposits to add armor to a unit. Have you ever dragbased or otherwise mass spawned on Konu, only to find ore blocking the spawns? Well... vehicle mining takes multiple turns. NAA not only doesn't, but makes the probe doing it stronger each time, allowing it to survive bigger and bigger pulls. This clearly wasn't the intended main purpose of the mod, but it's a very good use of it.
10. If you're using a unit for one purpose, mod it for one purpose. If your goal is to transport ore at the fastest possible speed, speed mod the hell out of a loggerhead, maybe including ONE defense mod. Something else can pull bandits out of the way, or you can let your base deal with them.
11. Mods, vars, and merits do not exist in a vacuum. The best units make good use of all 3, and try to complement them. Scroll up to the HT/Cerb combo. It's pretty strong on its own, right? Well, what if the unit is also RS. Now pilot it with a unit with both energy specialist and Engineer. That's a ginormous shield with insane regen, and you've still got 2 mod slots to play with.
(Note: In normal situations, this is overkill. When shielding matters above all else on the other hand...)
12. Capitalize on strengths, and make use of weaknesses. Many mods are stronger than normal, but come with a drawback. Sometimes though, the drawback doesn't matter. -25% shields on a Battle Axe? -25% of... oh right, nothing. Supernovas give +8 damage to energy. Well, that's awesome no matter what you're using, but there's a great way to make it even more awesome. The punisher is 2 guns, and yes, that +8 is going to apply to both. Etc.
13. Cost matters. You can make a VERY powerful unit if you get a perfectly varred and crewed advanced unit with 2 I mods, while also employing Shak mods. You're also going to pay more than a + unit for something that's much easier to kill. That's not to say that expensive units don't have their place, but if you spend 3000 TB on an army... yikes, that's painful for ANYONE to lose a battle with.
13b. Additionally, sometimes it's better to use 3-4 not quite optimal units in place of 1 perfect one, as the total cost will be lower, and the total performance will be higher. Of course, the CE is going to go way up too though.
The bottom line: Budget most definitely IS a factor you have to consider, especially when weighting your odds of the unit surviving a fight.
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Ok, let's put all of this together in a few examples.
Example #1: Newbie leveling with a MiteSo, you're pretty much just starting out. You're level 2 or 3, and you want to quickly work your way up to having access to the good units. With limited piloting and gunnery, you've decided a fast energy unit is the way to go, and it'll have to be a simple. You're either just starting and have very limited command, or you're trying to train multiple crews at a time, so you need to watch the 5k CE limit. Because of this, you've decided to use only simple mods to avoid a CE penalty.
There's 3 obvious choices here - the Sai, the Copperhead, and the Mite.
Let's look at the base Mite.
20+5 shields, 2 armor, 5/5 speed, and 2 2 damage, 1 cooldown energy guns.
It has a better shield than pretty much any other simple, but a measly 2 armor, average speed, and utterly pathetic damage. Clearly, something like a Sai or a Copperhead is going to wipe the floor with this thing, as both are faster, harder to kill, and deal more damage, making the Mite well... pretty pointless. Let's fix that.
Merits: Since this is a newbie leveling unit, we can safely assume that whether it's you getting those first few commander levels or leveling a crew, that whatever is piloting this isn't going to have any merits... so let's completely ignore those for this example.
Vars: Clearly, A and M are useless here. DRS seems like the obvious choice, as after all, E can't reduce a cooldown that's already at 1. However, this assumes you want something super cheap... so let's only do 2 vars, and let's take DE. E may seem like an odd choice, but you'll see where this factors in.
Mod #1: Proton Mass Generator - This adds 20 shields. That's a nice boost in general, but huge on a simple. Mite has the largest simple shield, yet you're still doubling it. Additionally, it has a +15 shield recharge acti, so in a pinch, it's also a nice regen booster. The catch? You lose HALF of your armor. Wait... what armor? The mite has 2. We're adding all of that shield power and giving up a whole 1 armor. Win.
Mod #2: The goal is to level as quickly as possible, and get you (or the crew) off of Tariona. Let's slap on a Combat Analysis System for +50% exp gain.
Mod #3: Vertigo Energy Turret - It's a nice, cheap, 1 cooldown energy gun, and an obvious complement to the unit's existing weapons.
Mod #4: Maxwatt Energy Transformer - This adds 5 damage to each of your guns, but also adds 1 cooldown... or does it? All 3 guns were already at 1, this ups it to 2, but that E var you took brings it back down to 1.
Final unit:
40+10 shields on turns the acti isn't used, 40+25 on turns it is, 1 armor, 5/5 speed, 150% exp gain, and the following guns:
2x 2 range 10 damage guns that fire every turn
1 3 range 14 damage gun that fires every turn
Most bandits you encounter on Tariona can't break that 10 regen. When you encounter 1 or 2 that can, well... you've got a nice shield reserve, and you can crank your regen to 25 on the 5 times when you need it most. You're not very impressive on range, but you can pump out 34 damage/turn (more if you get super close), and you can easily use that speed to get in range to do so. You only needed 3 mods to achieve all of this, so you're getting 50% more exp too. You're also doing it with a dirt cheap unit that you get the funds for even with vehicle mining (but don't - we'll supply this).
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Example #2: The Walking Shield (Aegis)This is a much simpler example. The Aegis is designed to take hits for other units, using a massive shield reserve and some damage reduction. So, let's make one do precisely that. Let's assume that this is going to be protecting a stack of squishy advanced units - perhaps sentries or lightfoots, and so the cost of integrating once (but not twice) is worth it.
Merits: The ideal merit combo would be Engineer, Energy Specialist, and Speed Demon - Get more shields, refill them faster, and add to speed. You of course can't always get the exact combo you want, but you'll want some mix of those.
Vars: RS, nothing else really matters
Mods: That HT and Cerb combo I mentioned above? This is a great place to use it. Since protons flat shielding applies before HT and Cerb, let's throw that in to boost the combo. Armor really doesn't matter on the Aegis. Slap on a Hydra to avoid slowing down what you're protecting. For the 5th mod, you might be thinking kite, but at this point, there's better answers:
-Sanc Dampening - With the shield already so huge, upping the built-in 3 damage reduction to 5 could be quite nice
-Energy Defense II - On the other hand, close range energy attacks can get through a shield no matter how huge it is. This will slow that damage down.
Result: You've got a massive walking shield protecting other units, it's fast enough to not slow them down, and it's either got good overall damage reduction, or lighter overall reduction with heavy energy protection.
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Example #3 - Aldus Beast LevelingIMPORTANT! - The new Aldus has been shrunk way down, with the Shak rate turned way up. This really doesn't work there anymore.[/b] (A similar build works fine for Dom/Hell dragbasing though.)
So, you're high enough level that you're willing to attempt the most difficult form of bandit grinding - fighting on Aldus with a stupidly weak Beast. You don't mind paying a huge upfront cost, and you're planning on using a LOT of command spam - this is for 200% exp stacked with the Aldus multiplier for 360%. You do, however, have to actually survive in this crappy meka to make use of its xp multiplier.
Vars: DE are obviously the critical ones. I'd recommend S for the 3rd, although M and R are also options if you want to involve slightly less command spam (saving you some Ammo Drops or some Power Bursts respectively.)
Merits: Acti Master and Eagle Eye. If you're willing to do a merit reset purely for this, switching back when you're done, I suggest Zerk for a 3rd merit.
Mods: There's aren't any obvious combos for this. The Beast has no strengths! You're pretty much going to have to brute force this one. Here's the 6 mods I use, and my logic behind each:
1. Wraithunter - It's not cheap to say the least, but you simply can't get a stronger energy mod.
2. EMP Cannon - This is generally the 2nd most powerful energy gun. Oblit shoots further, but you're fighting Aldus bandits, so you have to be in range of other stuff anyway. Additionally, since the EMP cannon does 150% damage to shields and WH does 150% to armor, there's an obvious combo here.
3. Hightower - This one's self-explanatory... the base shield on this thing just isn't going to cut it.
4. SBG - I picked this over Cerb, as preventing damage is critical.
5. Hydra - Even with speed spam, a speed of 1/2 isn't going to make that exp bonus worth it, at all (and will make some long range units basically impossible to kill). This kicks that up to 2/4, and 8/8 with all speed commands active, 5/5 while Fall In is cooling. That's quite managable.
6. Combat Analysis System - As the whole point is the doubled exp, well... that doesn't work without this.
Despite the huge cost involved, this isn't a very strong unit. A beast simply isn't going to be very strong, no matter what you do to make it not suck. However, with a weapon combo, ok speed, and and plenty of defenses with the aid of command spam, this is a unit that can generally hold its own on Aldus, and level you up enough to stop using it. It's pretty much the opposite extreme of newbie grinding with a Mite.
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Conclusion: This is a topic one could write a freaking book on. There's always new stuff to try, and no one knows ALL of the good combos, as there's thousands of them. However, if you think about what you want to do, find a good unit to do it, and mod, crew, and var it intelligently, you'll get a unit that does what you need it to do. Good luck, and don't be afraid to ask for help in faction chat, whether you're having trouble figuring out what you want, or just can't quite figure out what should go in that last slot. Good luck.