Web drones: Short version? They're terrible. Don't use them, particularly the light ones which are the ones you might be most tempted to use. Long version? The web drones are affected by diminishing returns the same as any other EVE module. Light web drones reduce speed by 5%, mediums by 10%, heavies by 20%. Pilot stoicfaux summed up the problem admirably with this table (which I've modified for clarity):
|# of drones||Light||Medium||Heavy|
The numbers reflect the target's speed after the effects of the drones. So if you're tempted to use five light web drones, don't: you'll only be reducing your target's speed by 13%. Five heavy web drones -- which are slllooooww to catch a target, if they ever do -- affect your target like having one web on it. And there's absolutely no reason ever to use more than three web drones of any type. I can kinda, sorta see mixing web and TP drones in a PvE mission scenario. Three medium web drones and two medium target painter drones might be useful for some missioning ships, such as Amarr or Minmatar battleships. Would they be more useful than the equivalent number of medium combat drones? I doubt it.
Salvage drones: These are pretty interesting! They're going to be most useful in a PvE scenario, obviously, notably in any L4 battleship that has the extra 25m3 to carry a set. In PvP, I think they're going to be most useful in ships with a lot of utility drone space, notably the various Gallente and Amarr cruisers and battle cruisers (and to a lesser extent, battleships). I don't really expect these will come into their own until CCP really rethinks the drone bays of the battle cruisers, HACs, and recons, though. Once that's done, I think they'll be more generally useful. For the moment, drone bay space is too small and too precious in most PvP ships.
Drone Damage Amplifier: If your ship relies on drone damage for the majority of its DPS, you should have one or two of these. For the time being, though, three is almost certainly overkill. Pretty simple.
T2 Armor Plates: Previously, these were inferior to Reinforced Rolled Tungsten plates because they provided no more armor HP and significantly increased ship mass (and to top it off, they were more expensive than the meta4 plates, too). Now, they have been buffed such that they provide significantly more armor HP... still with the mass increase. As a result, these are now excellent for "like" size ships, but terrible for undersize ships. Example: you should refit all of your plated battleships to T2 plates, immediately. On my Apocalypse Navy Issue, for instance, upgrading to the T2 plate adds 5k EHP and only reduces its speed by 4m/s. However, the same plate on a Proteus, while adding some 10k EHP (thanks to resists) also reduces its speed by nearly 100m/s. Similar effects are found with the other T2 plates for their respective size ships.
Target Spectrum Breaker: These put on a nice light show, but aren't very useful. Where I think they're the most useful is for solo battleship PvP, particularly what Rote Kapelle calls "Bushido" doctrine battleships partciuarly using multiple armor self-reps. That's hardly a mainstream market, though. I think CCP should open this module up to more classes of ships. It's a natural for recons and stealth bombers, for instance. I could also see it being very useful for industrials, though the cry of rage from gate-campers would be something to behold.
Capacitor Batteries: These received a buff which causes a "reflection" of any attempt to neut or NOS you. The reflection is nowhere near strong enough to be a factor in thinking about whether to fit one of these or not. The CPU these take is still the limiting factor; it's still far too high on these to consider them for 95% of scenarios where they might be useful. They remain a niche module mostly useful for scout ships and a few PvE logistics fits. When I lived in Great Wildlands, I fit these on my Covert Ops ships routinely to counter all those long warps over there.
Various new dead-space remote reppers and energy transfers: These are pretty awesome and you should not forget about them when you're fitting the new T1 rep cruisers and frigates, particularly for PvE. Don't neglect them for PvP, though. They're still very cheap, by and large, which makes them a viable choice for experienced pilots.
Reactive Armor Hardener: I started writing this part of the post and before I knew it, I had enough text down to be a blog post in its own right. So instead I'm going to jump straight to my conclusions. If you're interested in how I reached them, say so in the comments and I'll consider writing a Reactive Armor Hardener blog post. ;-)
I think the RAH is exactly as useful on the modern EVE PvP battlefield as any other meta0 T1 module, which is to say: not very. If you can absoultely ensure your enemies are going to come at you with only one type of damage, by all means fit it. For instance, I fit one to my Abaddon when I thought I might fight I-RED in it because I-RED only flies Amarr ships. It made sense. Since they were only going to be firing EM/Thermal at me, having 40% EM resist and 20% Thermal resist in one module was quite a useful proposition! But for most situations, the T2 EANM is a far superior mod. If there was such a thing as a T2 RAH, the decision would be a lot harder, but for now, it's not. The same argument applies to wormhole and incursion PvE.
In mission and ratting PvP, though, I think the RAH has a lot going for it, and it's for exactly the reason above: you're only going to be facing two types of damage, so it makes total sense to have all the resistance to those types of damage that you can. So definitely go ahead and fit it, particularly when null-sec ratting in armor ships.
Micro Jump Drive: I think the jury's still out on this one. The obvious application to using this one is in a fleet of armor-tanked sniping battleships. If someone scans you down and a fleet looks ready to land on you, the entire group activates this mod and scatters. You'll still lose a few ships as the module winds up but better that than to lose a whole fleet. I could also see it being very useful in ultra-small gang skirmish battleship scenarios, again as a GTFO maneuver. However, the CPU use of this mod makes it tough to also fit a prop mod, so I'm not sure I currently see it entering widespread use. But again, the jury's still out.
Ancillary Shield Booster: I've already written a ton about this mod in various posts, particularly FOTWs where I suggest its use. Where this mod is most useful is two scenarios: solo PvP (where you should be using one or two of these mods), and very small gang PvP (where you might use one). The former is ably represented by Rote's Bushido tactics, the ubiquitous solo dual-ASB Hawk, ASB Cyclones, and like ships. The latter is represented by the Sleipnir fit I flew in AT10. In that case, you're using the ASB to supplement your on-field reps. Your ability to burst tank in this situation will often cause the enemy FC to call a new primary since he isn't breaking you... while you reload your ASB. Larger fleets don't have to bother with this: they just bring more logistics ships.
Processor Overclocking Unit rig: Finally, this is easy to forget: there is now a rig that increases CPU! That said, the times you want to use it are fairly limited. A lot of the times you want to consider it are when fitting one of the modules above. Most of the new modules are pretty CPU-intensive and sometimes the CPU rig is just want you need to squeeze them on.
And aside from some of the mods that have gotten T2 versions lately (the Drone Link Augmentor and Drone Navigation Computer come to mind, as well as the Small Tractor Beam and the Warp Disruption Field Generator), I think that's pretty much it. Did I miss anything?
EDIT (3/Jan/2013): Added T2 armor plates.