Good question. You mean the .aj files, I am assuming...
Two schools of thought on this, and originally I was on the "don't check 'em in" side.
If you don't check them in, then everyone who wants to build has to run the Roo shell to generate them. That includes continuous integration tools. While it's boilerplate code, and can be annoying to have to check in, the advantage is that you don't need the tool to build it later.
I'm now on that side. I had that angle explained to me by someone from the Roo team and it made good sense.
Just remember to do a svn status or git status to see what changed recently before updating your SCM files.