SNESemu: No custom keymapping, no saving, but fast - 20 FPS in Zelda, 24 in Super Punch-Out!!, etc. Transparent layers are displayed as solids, causing visibility issues in some games.
SNES9xGP: Has saving and keymapping, but 0.95b release is slow; 12~15 FPS in most games. The next update should improve to about 15~20 FPS, though the project will die if the source isn't released (no more updates are planned). Most RPGs (Seiken Densetsu 3, CT, and FFs) should be fine; Mario RPG's SA-1 chip will likely cause heavy slowdown.
In fact, here's a general list of games that will run slowly or not at all for various reasons - sadly, many of the best SNES games are sluggish or unplayable:
Mode 7-heavy:
Super Mario Kart
PilotWings
F-Zero
F-Zero 2
DSP
Super Mario Kart
F-1 ROC II
PilotWings
Capcom C4:
Megaman X2
Megaman X3
SA-1:
Super Robot Wars EX: Mashoukishin/Lord of Elemental
Super Mario RPG
DBZ Hyper Dimension
Kirby Super Deluxe/Fun Pak/Super Star
Kirby's Dream Land 3
SuperFX:
Stunt Race FX
StarFox
SuperFX2:
DOOM (but we've got an even better port already)
Super Mario World 2: Yoshi's Island
Street Fighter Alpha 2
StarFox 2