I am a self-confessed Linux noob - But I am completely confused and overwhelmed by the idea of Gnome or KDE.
What should I choose? Whats the difference? What are the pros/cons?
This is a highly subjective question. As you're new to linux I'd suggest using the default install on the distro you've installed, get familiar with linux and then look into the various alternative dekstops/window managers.
In a very general* sense I've always found KDE to be closer to Windows in it's look and feel, where as Gnome is more like OSX, or even older systems like the Workbench on the Amiga so if you're familiar with Windows KDE may be the way forward, but if you do a lot with other stuff (probably not as you're confessing to being a linux noob) then Gnome may suit you more.
*As Geoff says this is very subjective and frequently comes down to personal preference so no down votes please people!
I think it depends on user preference. Do try both and see what you like.
I started out with KDE, but now my preferred WM is Gnome. My experience:
If you install both on your system, as most distros do, you are set. Both will run programs from each other and such. You might get a trouble with copy and paste between kde and gnome, but it should work.
The log in to kde and use it for a day or 3 and then gnome and use it for a day or 3.
Then make up your own mind. Don't get carried away with useless and damaging bickering.
For my 2 cents, being a redhat/fedora/centos person, I usually just use Gnome because it is default. Most of my work is in terminal anyway, I like GEdit.
But use what ever you like. If you install both, it really does not make a difference
Each window manager has different options and tweaks. The best way to find out your favorite is to work with each of them for couple of weeks.
Differences?
Applets can be found here:
Your personal settings are the key to get window manager work well.