Here are some mods that I find useful:
Raids
Omen is a must. It allows you to track and manage threat. Everyone needs to use this mod if you are raiding or running instances. It loses some utility if everyone is not using this.
Bigwig is great. See Solstar’s post for a list of features. I like getting the cooldowns and other information it provides. Littlewigs is a good addition to this because it adds information for the bosses in all the Outlands’ instances.
Decursive is another must if you have those abilities. As a healer I don’t always have time to decurse someone but this mod makes it much easier to do it when I can.
Other mods
I use Atlas loot, Cartographer and MapCoords. They provide lots of good information. I really like Itemrack. It allows me to switch quickly between sets of gear.
I cannot say enough good things about gatherer. This tracks all my mining and herbalism nodes. I use gathersync to send the data to guild-mates. Auctioneer and its addon are great as well. Scanning the auction house takes much less time now. I scan daily so I always know how to price my auction items.
Guildgreet extended is great for me. It’s not completely compatible with 2.3 so I have to disable it before accessing the guild control functions. This provides me with a pop-up telling me when guild-members log on; when they level or have been promoted. It connects alts to mains because I can’t remember who everyone’s alt is some days. It can be set to send greetings automatically but I don’t use it that way. It is especially valuable to me when I’m in an instance and may miss someone logging on.
Mass Resurre...
Guild Level 25
I hate running all over and not knowing where a mob is going. 

