One suggestion would be to allow users to write a manual sorting order for channels eg in a text file - although a nice little GUI list should be easy enough in Cocoa. I connect to twenty channels across multiple servers every start-up and, well, the automagic ordering tools just don't suit my fancy.
I'd like to be able to specify ordering by text file. This is the only real way I could see it functioning "as expected" due to the fact that Colloquy isn't aware of some of the channels I autojoin. The reason for this is that I use a few nickserv services for authorization and autojoining thus colloquy doesn't have a list of all channels I will autojoin.
I'm sure this wouldn't exactly be trivial to implement but it could be done as a single function to be run by the user - eg - "Sort Channels" that the user could call manually once all channels were opened. Again this is the only real way I could see it functioning "as expected" since Colloquy doesn't have a full list of channels to be joined.
Or does it? One alternative would be to compare the list of channels given by the user and to sort only AFTER all of those channels are opened by Colloquy.