If you can figure out what album you're listening to you can edit the ID3 tags containing your artist and album info from within the Zune software. Click a group that belongs to an album and then right click and Edit Track Info. That'll at least let you set the artist and album on it. Once that's set you'll be able to change the track titles by hand.
However you'll still have the problem of them being in one big folder in Music/Zune. If you apply album art though you can probably figure out which files are which and start moving them into folders based on the artist.
At this point though I'd consider just re-ripping them...If you put the CD in an its not recognized (I've had that problem with some obscure or new albums), then you can do the same trick as in the first paragraph. Go in and click all the tracks, right click, set your artist and album and then hand enter the track names. If you do that it'll rip them to the proper Artist/Album/XX Name.blah that you'd normally see if it finds the album info on its own.