For professional level engines, I run Houdini 1.5 (I imagine newer, paid versions of Houdini work as well) and Stockfish in SCID. The Houdini exe loads fine in SCID so long as wine is installed and the exe has been made executable. Both work very well for me, but I find Houdini's evaluations (e.g. -0.71 is a clear advantage to Black) to be the most meaningful. Stockfish evaluations are often inflated/optimistic (-0.71 might only mean a minuscule advantage to Black or +1.5 might not mean White is winning, but that Black in fact has strong compensation for the exchange. In my opinion, Houdini is particularly good at evaluating compensation for material deficit. I've tried the Toga, Fruit, and Glaurang engines; they are fine and , to my recollection, work well with SCID, but not as strong as Houdini and Stockfish.
For a simple chessmaster equivalent program, pychess (in the Ubuntu software center) might be suitable.
I also use Jin and Dasher in wine for ICC. I haven't tried FICS much.