Factorization. those routers are a godsend when you need to insert/pull items from banks of similar machines, even from specific slots
Thermal Expansion. the cyclic assembler is badass for rapid fabrication of items, all the machines are pretty awesome. tesseracts are vital for moving things around without cluttering up the map with pipes/wires
Buildcraft. pipes, pipes, and more pipes. gates/autoarchic gates help with automating things
MFR. tree farms, mob spawners/grinders, generating fertilizer, breeding animals, biofuel, and the all mighty deep storage unit. laser drill is awesome when your too lazy to go mining for ores. rednet is pretty awesome too, at least a nice stand in for the missing redpower stuff we all miss from ultimate
Soul Shards. when we need lots of mob loot, those soul cages are the way to go
Extra Utilities. cursed earth rocks for dark room spawners. the bud block is awesome for reed farms. iron spikes makes mob spawners even more efficient, and adds in rare mob drops youd only get if you killed them yourself (minium shards, bags of loot)
RailCraft. steam. massive storage tanks. all sorts of awesome rail automation. and some very cool decorative blocks (fitted abyssal stone my fav)
IndustrialCraft. nuclear power. solar power. generators. wind mills. water power. and all sorts of machines to grind, macerate, compress and recycle all those extra things you dont know what to do with.
Applied Energistics. amazing for automated production and crafting, pretty powerful system when you need to automate complex processes that cannot be handled with crafting grids.
ComputerCraft. turtles, the most amazing little machines ever. dig, chop, mine, craft, do all sorts of cool tasks. add MiscPeripherals and you get all sorts of neat little robotic minions to do your bidding.
Forestry. lots of stuff here dealing with trees, bees, butterflies. has a cool multifarm device. bee breeding. add ExtraBees and MagicBees and you can produce pretty much any element in the game
MystCraft. bored with the overworld? generate some new dimensions! if your lucky youll roll out a nice dimension that will provide some cool traits like diamond veins, nether fortresses in a desert, etc.