X-Perl has been my go to player frames mod for the last couple of years. I first started using Perl Classic and eventually switched over to X-Perl.
Questing / Map:
My favorite mod happens to be Carbonite Quest. It has, by far, the best map interface which is a true joy to use.
I used to use TrinityBars for my action bar mod. When 3.0 hit I switched over to Bartender4 and haven't had any problems. Love the simple functionality.
Gladius is by far the most important mod to have while playing in Arena. The most important option is the display of when enemies use their PvP Trinkets.
Kharthus's Hunter Timers
These informational mods are crucial for PvE and very helpful for PvP.
DoTimer is a great cooldown mod.
Power Auras Classic is the best graphical notifier of when procs happen (i.e. Lock and Load).
NeedtoKnow is my favorite mod for tracking debuffs on a target (i.e. Hunter's Mark, Serpent Sting, etc.).
RangeDisplay is probably the best range display out there.
A much improved talent display that makes the in game like Wowhead.
Advanced Trade Skill Window
Diablo 3 dynamic Orbs
Advanced Trade Skill Window is a time saver when it comes to professions, and it makes the display of the details of my profession much easier to read.
Diablo 3 dynamic Orbs is the best UI art that I have in my arsenal. It is also very functional. It looks awesome and helps me realize my health and mana easier.
SpamMeNot is my spam fighter. I haven't recieved a single gold spam since I started using it about a year or so ago.
Deadly Boss Mods
Deadly Boss Mods is a godsend in helping notify me of important events in boss fights. I've used DMB for a very long time and swear by it.
Failbot is a more recent addition to my library of mods. Failbot makes it easy to tell who in my raid keeps failing at different things (void zones, negative/positive charge, Heigan dance, frogger, etc.) by displaying "
These three mods are essential to anyone who uses the auction house daily.
AHsearch allows me to save any auction house search that I want and categorize it. This makes it so I do not have to type in my many different auction house searches.
Baud Auction makes it so I can sort the results how I want to (Buyout per Unit), and displays the results all in one page that is scrollable.