I think the source for minecraft servers is intended to be closed (You should not be able to even obtain it).
However, source for modded servers might be open, check Bukkit and similar projects.
Keep in mind that if you were able to find an open project, and you decided to add or delete various things, you are SOLELY responsible for ensuring that clients can still connect and operate properly.
Projects like Bukkit can be modified by writing your own plugins, so unless you want to REALLY change how minecraft operates (by adding new blocks or something!), you should be able to just write your own plugin without laying a hand on the server source code.
I admire your enthusiasm, but make sure you know what you're getting yourself into! :)