You and your brother can each have your own library on the same computer.
First, I'd make a folder somewhere for the new library. Put it in a decent location. Then, decide who will get the already existing library.
After you decide who is going to keep the current library and who will get the new one and you have created a new folder, hold down the shift key on your keyboard and open iTunes. iTunes will then let you create a new library. Use the folder you just created for this new library. After that, I would suggest using a folder within the new folder for all music for your brother, even if you like some of the same songs. It's best not to share music files, or playcount, tags, etc. can get messed up.
From then on, whenever you want to switch to another library, hold down the shift key while opening iTunes and choose which library you want to open.
Another simpler but less-effective way would be to create playlists and use the "sync selected playlists only" for each iPod. Make lists of stuff you want and don't want in playlists and only sync those playlists.