There are only a few that I could think of that could 'damage' the OS, unless of course someone wrote a program to do that very thing...

Those would be things like the sixaxis driver, or bootmenu, or anything that messes with udev or init scripts.

From what I have noticed, most of those all have warnings on them saying that they could cause issues.

The worse 'damage' that I've had, is the rootfs becoming full, and not being able to easily tell out of the 50 apps I just installed, which one is hogging it all.

Fortunately that Storage app fixes that issue.

This really should only be an issue if things that are in Extras are hosing the N900. Since Testing and Devel both have warnings saying that they very well could hose it.

slaapliedje