[Samsung Galaxy Nexus] mskip:
If you goto settings, about phone then it will tell you all about your current rom build. If its a yakju build then its a stock google rom and can easily be found and reflashed via my ToolKit. If its been put on by your operator then you wont be able to obtain it online and you are best backing it up (unless you dont mind putting the google stock rom back on).

To do that you will need to set your drivers up first. This is important as nothing else can be done without this step. If you have Windows xp or 7 then its pretty easy, you can install the drivers automatically via the GNex ToolKit, then reboot your pc. Goto settings, developer options on your phone and tick 'usb debugging' then connect the usb cable to your phone (with it booted into Android). This should install adb drivers which are needed for communication when your phone is booted into Android. Start the ToolKit and select your current build version (which can be found in settings, about phone). At the top of the Main Menu you should see a serial number under adb mode which means your device is recognised in this mode. Select reboot options (19) in the ToolKit and Reboot phone to Fastboot (3). This is a bootloader mode for the phone outside of Android where you can flash and manipulate certain parts of your phone. As this mode is at a much lower level then the operating system it can be your saviour if your phone locks or wont start and you need to flash back to stock.

Once the phone has rebooted to fastboot mode the fastboot drivers should be installed on your pc. If nothing happens try unplugging and replugging the usb cable to initiate the drivers. If the drivers have installed before the ToolKit refreshes then you should now see the serial number at the top under fastboot mode this time. You NEED both fastboot and adb drivers installed on your pc for everything to work.

After the drivers have been set up you will need to Unlock the Bootloader to be able to have access to system areas on your phone. BE AWARE that unlocking the bootloader will erase EVERYTHING all data on your phone including the Internal Storage (virtual SD Card) so copy anything you need to from your Internal Storage accross to your pc and use the Backup option in the ToolKit to save any installed apps and associated user data that you want to keep. This is done in adb mode so your phone will need to be in Android.

If you want to back up your current Rom then Unlock the Bootloader, reboot your phone into Android, go through the setup quickly (as the phone will have been wiped), then goto settings developer options and enable usb debugging. Start the ToolKit and in the Main Menu select 19, 3 to reboot back to fastboot mode. Then you can BOOT into CWM Recovery without flashing it (9) and select backup/restore to backup your Rom/user data/boot image to a datestamped folder inside a folder called Clockworkmod on your Internal Storage. The rebooting into Android step after unlocking the Bootloader is important as cwm will not work properly without doing that.

Once that is all done you are ready to reboot into Android from cwm, get back to fastboot mode as before and select 1-click option (7). You will get a message on the unlock stage saying that your device is already unlocked but then it will just skip to the next stage. Be aware that when the device boots into Android the first time this is to let the user enable usb debugging for adb operations and if you have already done this then the ToolKit will wait for about 3 minutes before carrying on. Be patient as the ToolKit hasnt frozen, its just set to pause before carrying on.

Ok now thats all over with, on to your other questions lol. I would advise trying either romanbb's AOKP (build 24 should be up today) or bigxie's Apex 1.02 to start. Personally I use Apex as it has loads of customisation and runs very well but saying that I will be trying romanbb's new build when it is out.

Kernels are like the drivers of your phone. They set up how it works and what it can do. Custom Kernels can give better battery life and more power, performance, stability so its well worth trying them once you are rooted. They will tell you what builds they are compatable with but if you are thinking about the above Roms then you will be on Android build 4.0.3 and most new kernels work with that. I use franco's kernel but there are ALOT of established kernel developers working with the Nexus so you could try fugumod by nikademus or trinity by morfic. These are all flashed via cwm (download file, copy to Internal Memory, reboot to recovery mode once you have cwm flashed). You can enter cwm by rebooting to fastboot and using the volume buttons to select recovery, then press power to select, or from the reboot phone options in the ToolKit (19,4 in adb mode).

Bootloaders and Baseband/Radio updates are something to think about but not really needed if your phone is running fine. You wont notice any change if you update the bootloader as its just like updating your bios on a pc. Just gives some extra functionality or updates some deep down settings. Radios control the communication part of your phone and updating to a new one may improve battery, signal, wifi, gps lock. You can update them by either grabbing a premade zip and flashing via cwm or download the .img file and flash that via the ToolKit.

Dont worry about malware included in custom roms as long as its by an established developer. They would never put anything dangerous to the end user in one of their roms as it would harm their reputation and if anything was found by a user the rom would be taken down imediately by us mods :) to keep you safe.

I think thats everything you will ever need to know lol. Sorry theres alot I wanted to make sure you had all the ammunition you needed to continue and it took soo long to write I had lunch half way through :p

good luck.

Mark.