Mods can do quite a variety of things, from purely cosmetic to purely functional. For example, you can get a bar mod that lets you reposition your hotkeys. Below is a list of mods that I personally use or think are useful that will help you out in PvP in one form or another. I'm leaving out cosmetic mods (like bar mods), as you can find info about them elsewhere.
If you'd like to download versions of my UI, click the link to the left.
If I'm missing anything you think is useful or find a dead/outdated link anywhere, let me know!
Natur Enemy Cast Bar
This will show duration timers on abilities your opponents use. For example, if an opponent Divine Shields, you can time a cast such that it will land exactly when the shield drops. You can also hit a rogue as soon as CloS drops. You can download it here.
Power Auras
This is a very handy mod for PvP. This will allow you to set up a graphic to show when a buff or debuff is on you or your target. For example, I have a big exclamation point set up to show when I have Hypothermia, so I know if I can snap/block easily. I also have a big snowflake appear when my target is frozen. It's very versatile and can be useful for any class at all. You can download it here.
Also check out the left sidebar for a tutorial on how to use it.
Arena Live Frames
Keeping the old description from ArenaMaster mostly intact as it applies just fine, but this mod has a MUCH cleaner and more functional interface, and doesn't require multiple people to have the mod to easily get all target information on screen.
As the name implies, this is only useful in arena... but wow is it useful there. When you click on someone, it'll add them as a target to a window for you, updating their health as the match goes on. You can click on a name to target them easily, and keep an eye for possible kill targets as health drops. At the start of the match, just pass your mouse over as many targets as you can to fill the frame. Absolutely amazing for arena and can definitely cut down on the overwhelming confusion inherent in 5v5 and even 3v3. You can download it here.
JIM's Cooldown Pulse
This is a handy little mod that will flash an icon of a spell as its cooldown is up. This is great for fireblasting on the run, or knowing when CS is available again. You can download it here.
Quartz
A great mod for a cast bar. This will show you when your cast will "really end", given by a red bar. If you have a macro that starts with /stopcasting, like a /stopcast and then Ice Lance, you can get an instant cast off faster than normal. This can be risky, as if you do it too early you'll lose your initial cast. With some practice this will become a rare occurance. You can download it here.
Mik's Scrolling Battle Text
Like SCT, but much slicker and better on performance. It also has a lot of very user friendly options and is VERY customizable. You can download it here.
Bongos
Absolutely awesome bar mod. It's very clean, high performance, very intuitive, and VERY customizable. Assigning individual keybindings to each of your hotbar buttons is as easy as holding your mouse over a button and hitting the key you want. You can download it here.
TinyTip
This allows you to put some custom info on your mouseover tooltip. Very handy. Download it here.
Pitbull
An awesome and highly customizeable unit frames mod. Moving your unit frames and your target's alone can make things much easier to keep track of. Also provides a focus unit frame, cast bars, and more! Download it here.
X-Perl
Another awesome and customizeable unit frames mod. It's a bit "fancier" than Pitbull, but I've switched to it and am enjoying it greatly. I'd recommend checking out both Pitbull and this to see which you prefer. Download it here.