
Here are the mods I use, if I use them for specific times/classes it is listed in parens.
Ace3 - Libraries
Align - puts lines on your screen to align UI components
Ampere - turn mods on/off in game
ArkInventory - bag mod
AzCastBar - casting bar, also have flight timers and swing timer installed
BadBoy - spam killer
BetterBlizzOptions - makes the Blizzard options frame movable and resizable
BetterInBox - modifies the inbox into a scrollable inbox, including open all options
BetterQuest - better quest log and tracker.
BigBrother (Raid) - keeps track of buffs, flasks, elixirs
Bollo - customizes your buffs frame
Bugsack - keeps track of any UI bugs so you know what mod is causing the errors
Butsu - loot frame replacement
ButtonFacade - skin UI buttons
ButtonFacade_Rothar - ButtonFacade skin
BuyUmAll - helps when purchasing items from vendors
Cellular - keeps track of whispers you receive
ChatKeys - allows you to assign key bindings to chat functions
CorpseInfo - shows if a player is online when you mouseover their corpse
DaHud - customizable hud which includes party, pet and focus frames
DayTrader - adds alt-click ability to item trading
DBM (Raid) - boss mods
Dominos - action bar mod
Fane - improved chat tabs
FramesResized - makes frames longer and movable
FreeMe - cancels Salvation buff while tanking
FriendsWithBenefits - sync friends lists between characters
FuBar - information bar with lots of plugins
FuBar_CraftTimersFu - keeps track of tradeskill cooldown across characters
I also use many standard plugins like bags, money, mail, etc...
GatherMate (Miner/Herbalist)- node tracking addon for miners/herbalists
GatherMate_Data (Miner/Herbalist)- load all known ore/herb locations
GatherSage (Miner/Herbalist) - displays information about a node in a tooltip
GuildCheck - shows who has joined, left or leveled in your guild since last login
HandyNotes - mapnotes
HatTrick - checkboxes on character frame to show/hide cloak/helm
IgorsMassAuction (Mule) - quickly auction multiple items
Incubator (Raid) - mob respaun timers
InstanceMaps (Raid/Instance) - displays maps of instances
ItemSocketingHelper - shows gems available when you mouseover a gem slot
LightHeaded (Leveling/Questing) - im game Wowhead quest notes
LiteAssist - assign key bindings to set an assist and then assist them
MagicTargets (Raid) - PvE status frames
Mapster - improved game map
Mendeleev - information about items in their tooltip
MobNotes (Raid/Instance) - notes about mobs in their tooltips
MoneyTrail - shows total gold for all your characters on the realm
MountMe - switches to speed enhanced gear when mounted
MSBT - scrolling combat text
NamePlates (Not a mod) - name plates graphics
oChat - simple chat mod
oGlow - adds quality borders to items
Omen (Raid/Instance) - threat meter
OmniCC - cooldown counts in buttons
oRA2 (Raid) - raid organization mod
oUF - minimal unit frames
oUF addons - Atal layout, Banzai, DebuffHighlight
ProfessionLinks - lets you see required mats for anything that can be crafted
RatingBuster - converts combat ratings to percentages in tooltips
RedRange - makes action buttons red if out of range
rFilter2 - buff/debuff tracking
SaleRack - gear switcher
SharedMedia - textures, fonts and sounds that can be used in mods
SimpleMP3 - in game MP3 player
SimplePriceEach - shows per unit pricing for stacked items on the Auction House
SLDataText - adds game information text to your screen
SmoothDurability - modifies the armored man and paperdoll frame
StarTip - customizable tooltips
StealYourCarbon - automatically purchase regeants
Talented - improved talent frame
tekGossipSkip - skips NPC gossip
tekJunkSeller - automatically sells grey items when you visit a vendor
tekKompare - simple item compare tooltips
teknicolor - colors names in chat by their class raid colors
tekPlayermenu - enhanced right click menu
teksLoot - group loot frames
TheLowDown - automatically scroll to the bottom of the chat window
Threat-2.0 (Raid/Instance)- library showing threat, I use this instead of Omen when tanking
VendorBait - shows most profitable item when completing a quest
VranxMM - my own modified version of the PocketPlot minimap
WitchHunt - spell alert mod