The algorithms class I'm just finishing now let me write my solutions in Perl. Basically, I'd write them up in my text editor, FTP them in, then connect via ssh and run them, storing my session text in a file. Not terribly hard, once I knew what the proper Unix commands were for all that.

I suppose you could do much the same thing with a secure server and user login system, but since you generally want to test your code locally before uploading it anyway, I don't see how this approach really improves things.