RetinaPad is AMAZING--well worth the $3 and then some for how well it works at making enjoyable again some of the iPhone apps I love that a year later still haven't been updated for iPad. (And as mentioned by others, it's fine with Winterboard...if you're not a thief.)
Black Keyboard is gorgeous. No, it doesn't work in Cydia or iFile--neither do most other theming-related tweaks, for good reason. Minor annoyance, not worth not picking it up over--especially since it's free!
FolderEnhancer is just as good on the iPad as on the iPhone. I'm down to a single springboard page because of it. Light years better than Apple's stock folder implementation.
Photo Albums+ is also just as good as on the iPhone, and fixes a stupid issue that never should have been there in the first place. Hello, Apple? Why wasn't this part of iOS4 and up?
Oh, and SBSettings. Again, one of those things that make you wonder why Apple is so stubborn about the more awkward parts of their UI. (or the ugly ones--see Black Keyboard)
(Also carried over from my phone, things like NoSpot, No Page Dots, PkgBackup, and iFile.)