How to manage applications without a GUI? Ubuntu Server

So I've been fascinated about the idea of having Ubuntu Server as my main file server and P2P machine (and perhaps even functioning as a home router). But then the question is, how can I control or access for example P2P programs without a GUI? Is that even possible? e.g. Transmission, Deluge, aMule, etc and the list goes on and on.

Such a lightweight operating system could serve P2P needs quite well too! Get spare hardware and underclock the hell out of it!