Honestly this is a hard question since I don't use mods. I guess I am excluded from this, however If I would choose 1 mod for MineCraft. I would most likely choose a mod that enhances MineCraft's Java script 3-D mode, or have the graphics be changed slightly to an HD texture. I rather say this is quite hard for me to decide over a mods... since again I don't use them very often.
Rei's still has some things I hope are added to it eventually like maybe being able to see other party members on the map, hopefully he implements that one day.
Mo' Creatues can be a little overwhelming because the creatures sort of spawn just everywhere, but if you we're able to pick and choose creatures here and there it would be awesome, I'd keep sharks and dolphins haha
I'd probably have to say Forge. Cuz without usage of Forge and FML, half of the modpacks and setups that we all use and love, like Aether and Mo'Creatures and IC2, and even the Technic Platform and it's packs, wouldn't exist. Or at least they'd be 4 times as hard to compile and implement to the public, I'd think.
Thaumcraft. Adding uses for useless items, very very interesting new mechanics and cool blocks, integration into everything, forces a healthy amount of resource management and encourages crop farming. Adds excellent items that actually DO something non mod-related, so you'll have an actual incentive other than "Because new mod." I just love it.
There are millions and millions of mods! So hard to choose from! I really enjoy Mod Packs, but if I had to choose my FAVORITE, it would be BTW, Better Than Wolves, it just adds so many cool, and helpful tools, and building things to make the game more enjoyable, but still user-friendly! Second would have to be Mo'Creatures, as the starter of this post even said, it adds a much more realistic feel to the game, adding a lot more mobs, to enjoy the game, and its true potential! I can't really think of a Third one, because there are just so many good ones out there...! But my favorite Mod Pack is for sure Magic Farm 2, as I am a big Farmer, and I love the hardcore aspect of it, while playing on the Mode Hardcore that is!
I highly recommended anyone who hasn't played Magic Farm 2 already, to go play it right now! Just click here to go to >Feed-The-Beast's< website to download the Launcher and play!
It allows you to transfer items in any direction you want unlike vanilla ducts and adds more item filtering abilities. With it I can make complex item sorting & transportation systems easily and with a lot more freedom for design. Like hiding your smelter behind a wall or underground, and just having chests for input/output/fuel. Or having a number of various farms with hopper collectors and having them all feed up to a collection chest somewhere else. It has really made my minecraft life much much simpler.