FPS lag? I'm gonna have to say any mod that you go crazy insane with in a single area, (IC2 cables, Buildcraft pipes, Railcraft's cart train sounds for some(if your sound is on), pretty much any large amount of custom rendering in an area, or thaumcraft's graphic effects).
Redpower has a particularly nasty FPS hit right now including something about the Relay and tick events. If at all possible, prefer to use Thermal Expansion for your transportation needs. Surprisingly enough, Gregtech's multiblock structures are unusually non-laggy, too.
Of course, your mileage may vary. All computers are different.
Things to avoid:
•Large amounts of Redpower Relays (use hoppers for now)
•Unnecessarily long amounts of Buildcraft piping(they're awesome for small, short jobs because of gates), prefer Liquiducts and Energy Conduits for long distances, or Tesseracts if you've got the pearls
•A ton of single stack items going through tubes or pipes(compact them first in a chest, buffer, regulator, etc and use a method to remove stacks at a time (EG. 4 filters + 1timer on your super fast quarry enderchest))
•Too many active timers (turn off ones you don't use! If you need to use them, use them smart. (EG. 1 Timer connected to 16 transposers, not a timer for each)
•Timers on rediculously short delays, use a computer or a turtle for this
•Huge arrays of solar panels or water mills, if available use compact solars or advanced solars if you're using the sun as your choice of energy
•Extrabiomes Redwood/Fir forests tree leaves on fancy... I use Optifine and turn on Fast leaves for this very reason
•If your computer is particularly not good, don't build a tier 5 soul shard blaze spawner in your house.. 250 blazes are laggy as hell with particles on
•If you absolutely NEED a cobblegen and have gregtech installed, grit your teeth and use the Electric Rock Breaker for some EU. It prevents the constant lighting updates that block breaking does (you still need lava, but it doesn't move)
•If your GPU supports it, TURN ON OpenGL, and if you have optifine, set it to Fast