Fairy-Stockfish
Strongest open source chess variant engine in many variants. Configurable for custom variants and trainable with NNUE (neural networks). Used by many chess variant websites such as Lichess, Pychess, Lishogi, etc.
Sjaak II
Configurable open source chess variant engine supporting a large variety of chess variants. Used to be one of the strongest variant engines, but it is mostly superseded by Fairy-Stockfish now, also because it is no longer actively developed.
Stockfish
Strongest open source chess engine, basis of many strong variant engines. Only supported variant is Chess960.