Multiplayer over the internet will always be 5 frames per second - the games haven't been designed around online play...
Four Swords is not a GameCube or Wii game - it's part of the Zelda: A Link to the Past/Four Swords cartridge released for the GBA - I played it successfully with my girlfriend on one PC though...
Formerly with VisualBoy Advance Link but AFAIR the VBA-M project (a revival of the original VBA with new features) has this feature built-in as well.
http://code.google.com/p/visualboyadvance-m/