I have to ask an engine-related question: after I installed the Stockfish 2.0.1 engine on my Winboard 4.5 beta, I can't analyze with it. What I mean is, it's giving nothing in the engine output; it can only analyze with the default engines that come along with it (Houdini 1.5a, Delfi and Phalanx). What may be the reason?
Stockfish is a UCI engine so it doesn't understand xboard as they are different protocols. As user @WesFreeman mentioned in the comments, polyglot is an adapter that can get UCI working under Xboard/Winboard. Perhaps visiting the Winboard Startup Dialog or reading the help file may assist you in resolving this issue.
Winboard can also execute polyglot internally if you use -fUCI in the command line, i.e.
xboard -fUCI -fcp stockfish -sUCI -scp stockfish
To download the required programs, you can type:
sudo aptitude install xboard polyglot stockfish