Currently, SpaceX has developed the Merlin 1 family (1B (Falcon 1), 1C (Falcon 9 v1.0), 1D (Falcon 9 v1.1/F9-R/Falcon Heavy), vacuum versions and sealevel versions) which are LOX/RP1 based. (75-145Klbs thrust)
They developed (and abandonded) the Kestrel engine used on the second stage of the Falcon 1, also LOX/RP1. (6.9Klbs thrust)
They developed the Draco and SuperDraco engines using hypergolics (monomethyl hydrazine fuel and nitrogen tetroxide oxidizer). (90 lbs and 15K lbs thrust)
The next engine on their list is the Raptor, which is expected to be Methane (CH4) and LOX based. (660Klbs thrust)
Do we know whey they chose methane over hydrogen? Performance wise, LH2 is usually the go to propellant.