Channel and Favourite Room Information should be moved to a seperate file in the Application Support folder.

[encro]

MVChatBookmarks and 'Chat Room ##room (irc.domain.net) Settings' should be moved to '~/Library/Application Support' as something like a separate connections.plist rather than being stored in ~/Library/Preferences/info.colloquy.plist

Separating the information in this way makes it easier to transport the channels to a new machine and if the info.colloquy.plist becomes corrupt you can delete this file to refresh the program settings and not loose your channel connections.