Guild Recommended Add-Ons:
Character Profiler: used in guild roster to track your character(s) information. (Installation Instructions)

PVP Log: used in guild roster to track your PVP activity.

Interface Add-On Bundles:
CT Mod: several small interface mods compiled into one package.

CT Raid Assist: just the raid assist add on from CT Mod.

X perl: a customizable complete replacement for Blizzard's default unit frames, including raid frames and raid tools, with many additions and improvements.

Cosmos: Cosmos provides you with many Add-Ons including but not limited to various toolbar AddOns, which provide additional toolbars to use (along with keybindings for them), QuestMinion to show more info on your current quests and progress with them, and DPSPLUS which provides a detailed breakdown of your DPS.

Titan Panel: Great interface mod that adds a control panel/info box on top and bottom of the screen that you can customize with titan add ons.

FuBar: Ace 2 interface mod that adds a control panel/info box on top and bottom of the screen that you can customize with FuBar plug-ins. FuBar and Titan Bar perform the same functions, which one is right for you depends on which plug ins you wish to use.

Battle Information:
Recount: a highly customizable damage meter that tracks your parties damage and is designed to help be a raid analysis tool. It tracks information on you and your party members to help you improve player’s performance. This is achieved via using graphs to convey detailed information on damage/healing done by each individual spell/move. It also shows time based data or pie charts to get a better sense of proportions.

KLH Threat Meter: it is exactly what it sounds like.

Omen Threat Meter: another threat meter option. Omen reads info from KLH if that is what the rest of your party is using. Omen tends to be more sensitive than KLH and reports more accurate data. Omen is also quite customizable and has options such as playing warning sounds when you top the threat meter and pulling out your threat up against one other persons.

Deadly Bossy Mods: Provides Information about raid bosses as well as PvP battle information.

Dr. Damage: This is a lighter version of TheoryCraft. It displays the calculated, average damage or healing of abilities with talents, gear and buffs included on your actionbar buttons. The addon will also add various information to the default tooltips in your spellbook and on the actionbar.

Crit Line: I know how everyone loves to break their own records of their hardest hits/crits. This addon saves your highest damage output and gives you a message when you break your records. There is also a titan panel version out there that gives you access to all your records from your titan bar. (this add on seems a bit spammy for the first day you use it because it is reporting all your hits but once you have it for a few days it becomes fun to see when you break your own records)

Misc. Add-Ons:
CCBreakWarner: This Add-On alerts you when a mob you have CC'd breaks free (even if hit out early) as long as you use a focus target macro to cast your CC spell. You will see a text warning and hear a sound effect whenever a CC spell you can cast fades off of your focus target. (Macro Instructions)

Auctioneer: Great auction house add-on, tracks auction statistics and item information. Also shows how much items sell for to vendors.

Spam Sentry Anti-Gold Spam: This add-on stops gold spam messages from showing. You can use a one-click report system to create a GM-ticket for the caught spammers. Both spammers and bots can be reported manually as well.

Rating Buster: The design aim of RatingBuster is to provide detailed, meaningful and customizable information about items so you can easily decide for yourself which item is better. This has a lot of configurable options as to what information is displayed so make sure to have a look at those to make the most of this add-on.

Atlas: The core of Atlas is basically an image viewer. However, it's the images that come with Atlas that make it worthwhile: a map for every instance in the game. Furthermore, the maps are marked with the locations of bosses and other points of interest. Atlas also includes maps of battlegrounds, dungeon locations, flight points, and outdoor raid bosses.

Atlasloot Enhanced: To go along with that fabulous Atlas add-on you downloaded here is atlasloot. Using this add-on you can see all the loot dropped by all bosses in every dungeon, faction loot, rep loot, BG loot and arena loot. This is an amazing add-on and a must have. After you have downloaded this there is never a need to spend hours looking up what drops where... just open up your atlas and find out in game.

Decursive: Say goodbye to targeting someone to remove their curse, disease, poison or anything else you can dispel. Decursive is a cleaning mod that helps each class that can remove afflictions do it with ease. This mod creates a small square on your screen that turns red when a person in your group is afflicted with something you can remove. You simply click the square, and like magic, the de-buff is gone.

Gatherer: This addon does not track like a tracking ability does, rather it "remembers" where you have found various items in the past. It does this whenever you gather (perform herbalism, mining or opening) on an item, and records the specific map location in its history. It also shares all items gathered from people in your guild and shows that info on your map as well.

Flight Map: FlightMap draws lines on the continent maps, showing you where you can fly from each zone as you mouse over them, as well as listing all the available destinations, their costs and their flight durations. Flight masters appear as small boot icons on your main map. During flights, a progress bar shows you how long is left on your current journey.

Loot Hog: Lightweight Addon to see /roll results in a sorted list. Loot Hog automatically counts and sorts Loot Rolls. You can Auto-Announce winner to Party and Raid. Display sorted list of all Rollers in chat. Ignore out-of-range rolls, Kick incorrect / invalid rolls.