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Forgot to mention Symcalc, which adds a very useful tool for determining the stability of your infusion altar. After playing around with it, I came to understand the cryptic mechanics behind the whole stabilizing feature. (seems the infusion altar checks a square radius around itself and the size of the square is determined by how you have your pedestals arranged.)
Cosmetic armor.
I like wearing my awakened ichorium armor set while looking like I'm wearing the Fortress Armour set.
Iron chests.
Small and simple mod, yet still so useful.
Ender Storage, translocators, wireless redstone, NEI.
All those mods by ChickenBones. I can't live without them.
Ex Nihilo.
Just started using it and I like it. Though time consuming, I find myself unable to stop hammering cobblestones and running gravel through sieves.
I was going to mention Glass Shards but @ljfa beat me to it
At the risk of repeating some, Inventory Tweaks is hugely handy; likewise MineTweaker - you can have it do very little or as much as you want.
I actually really like Enchanting Plus, if you want to go vanilla-ish with your armour - if you have MFR it's probably not needed (due to auto-enchanter and auto-disenchanter), but its very handy if you're more magically inclined.
Likewise, I have a quiet and deep love of Xeno's Reliquary. Again, its not to everyone's taste, but I love the various flavourful artifacts it brings into the game.