Make sure the new mobo is the rigth form factor for your case (microATX, ATX, or BTX, its usually ATX). Make sure your current components (ie processor, ram, gpu) match the new mobo. Also, you'll have to reinstall your os, so start backing up any data you want to keep
. If your using windows, you'll have to call them up and get a new key, too. Its supposed to be about a 30 min question anwser kinda deal, and they'll give you a new key. I think thats the major things to watch out for.
Also why would you want to just upgrade the mobo? Usually ppl upgrade the mobo when they upgrade to a new procesor that needs a different socket. Just wondering
Edit: forgot to ask if its a prebuilt? If it is then you'll have to get a new os too. The OS's that come with prebuilts are specifically for the mobo that it came with.