I use loads of mods, main ones being:
Flexbar (the BEST mods for remaking your button layout)
Ct-Mod
Ct-RA (needed in the high end stuff)
Stancesets (great for switching melee weapons on the fly)
Nurfed HUD (Means you can get rid of your player portrait and target portrait and gives you more space).
Gather (Records where you find nodes, herbs etc on your map).
Move anything (lets you move/hide almost every element of your UI)
All in one inventory (Opens all your bags as one big bag)
Auctioneer and lootlink (lets you scan the AH and store the prices of everything on there and updates the average prices everytime you scan. It then shows the avaergae start bid and BO prices in the tooltip of any item you mouse over).
It is a pain on patch day to update all your mods but if you know what you want it only takes about 30 minutes.
some screenshots of my hunters UI can be seen here:
http://www.fulltimewebmaster.com/myforum/viewtopic.php?t=694&mforum=con