There's the fsck command. But I don't know if that would do the same thing that your Windows check did. Also, I'm pretty sure you can't run fsck on a partition that's mounted, so I don't know that you could boot into Maemo on the N900 and then run fsck on the partition that you booted from. That said, normally a Linux system would automatically run fsck at startup to look for errors. Don't know if Maemo works this way, although obviously even if it does, restarting wasn't solving your problem.

Anyway, hope that maybe helps point in a useful direction. Perhaps someone more knowledgeable can make a better suggestion and/or explanation of fsck.