I'm using:
Bagnon - Makes your inventory/bank one window and shows how many you have of what item in the tooltip.
Cartographer - Nice map mod, has a somewhat buggy waypoint system, but I don't use it much.
Natur's Enemy Castbar - Keeps track of cooldowns/buff/debuff durations.
CT Core/Mailmod - I think there's better mail mods out there but I use this one anyway. I only use CT Core for alt+click buying stacks of food and vials, etc.
Deadly Boss Mods - For raiding, and it gives you timers in Battlegrounds for flag/bunker capping, or a win time estimate.
Grid - Health/debuff monitor.
MobInfo2 - Keeps track of enemy HPs and loot in the tooltip.
Omen - Threat meter
Outfitter - Wardrobe mod, switch gear sets with two clicks.
Parrot - Scrolling combat text, I can only find this mixed in with compilation mods atm. I know it was standalone but it seems to have been taken down. If you can't find it the normal SCT (from curse, not built-in one) is pretty much the same.
Preform AV Enabler - Synchronizes AV queues and shows what battleground everyone in the group gets.
Proximo - Arena helper, shows HPs/class, doubles as targeting/click-casting bar.
X-perl unit frames - popular unit frame mod. Standard stuff, 3d portraits, skinned bars, etc.