I would go with NetBSD (
http://www.netbsd.org).
It's UNIX-alike, much like linux, but one of the core goals of the NetBSD project is to run on as many different architectures as possible. If anything is going to run on your Classic II, it'll be NetBSD. You also have a good chance of running X11, check the NetBSD web site for info on your hardware. (I would bet you can get that zip drive working...)
If you are interested in programming in a UNIX environment, NetBSD is a much better choice than linux, IMNSHO. The combination of centralized control (linux is a kernel, NetBSD is an operating system) and a strong emphasis on clean design and implementation make NetBSD an ideal academic environment. Plus, OSX's BSD layer means much of what you learn in NetBSD will be applicable to OSX.
I have deployed quite a few NetBSD servers as intranet and internet servers in a variety of roles. There was some initial resistance from management, but when they saw I could take a P150 or a Powermac6100 off the junk heap and run a mailserver for a few hundred people, they saw the light....
The one con versus linux is that the user base is smaller. Seems like you can't open a web browser without finding linux HOWTOs... resources for NetBSD are somewhat more modest, but between the website and the mailing lists, there are plenty of smart people ready to help. The all text install may be a bit of a shock if you've never tried a free *NIX before, but it's nothing an experienced mac user couldn't handle (heck, it's no worse than your average PC BIOS).
Regardless, the more I think about it, I'm pretty sure your choice will be NetBSD or nothing. Linux is pretty intel-centric..... I wouldn't put money on there being a 68K linux..... ah, and a quick trip to
www.netbsd.org shows me that this mahcine is supported "console only" meaning no video. So there you go, it's either that or OS7
hope this helps...
-alex.