I just got a Galaxy Nexus and I want to revert it back to it's original condition for starters ( I'm talking about the software ). I noticed I have ClockworkMod installed, does that mean I have a custom ROM installed?
ClockworkMod is a custom recovery software. If you want to revert to the original ROM, then you can download the official ICS ROM for nexus and flash (install) it if you donot have a backup taken previously of the phone. And AFAIK, you can still root your phone again on ICS and then the phone will again be at your command (you can even install custom APKs). Also you can try a file manager like, Astro File Manager which I personally haven't used it but you can get it from marketplace and use it to install non-market apks by simply transferring the apk over usb to sd card and tap on the apk.
Generally, but not all the time, the presence of CWM which is a custom recovery, suggestively implies a custom ROM is present. But, having a custom recovery as CWM far outweighs the normal recovery that is found in the majority of handsets, some are limited, some are crippled.
You can easily flash another ROM such as ICS, or CM9 which is available to download. Hence I would highly suggest to leave CWM in there for a simple reason - to enable backup/restore of the ROM.
Judging by your previous comments in other answers above, it sounds like a unstable Jelly Bean ROM made its way into your handset.
Go to CyanogenMod site and get the download for either one of Nexus (crespo) or a Nexus 4G (crespo 4g) (crespo is a codeword given as the name of the handset). Whichever one is it you have, make sure you have the right version.
After downloading it, push that across to the SD-card, and use CWM to flash it for you. Be sure to wipe cache/data before hand. Yes, you will lose everything you have on that unstable Jelly Bean ROM. And then you should be back into the stability of the CM9 ROM.