FWIW there is a way to add in syntax highlighting, and I could probably create a new instance for that. There was also chatter on the Etherpad channel yesterday about writing plugins for compiling and running programs on the backend of the server.
Additionally, I suppose, we could write a plugin for enabling a grouping of pads into projects, which would make it easier to have multiple files open at once.
I think the major problem is that any files on the etherpad server will need to be downloaded or copy/pasted before you can actually run them, which may or may not be ideal. But again, there may be a solution in the plugin API.
("backend of the server" - sorry, I just woke up)