"Terminal Guidance" is (or should be) it uses it's active seeker to home on the target, i.e. the AA-12 actually isn't an "AMRAAMski" but it is SARH until it reaches say, 15 kilometers within its target then goes active.
"Target Memory" Useful for Anti-Radiation missiles it allows the missile to memorize the location so if the radar shuts off (which in-game it never does anyways) so it'll still hit. Useful for other things but that's how I always ascribe it.
"Home on Jam" means that if you fire a radar guided missile and the target aircraft starts to use it's jammer, it uses that as it's homing source, not the reflected energy of the radar.
"Optical Backup" means a radar guided system has an optical seeker just in case of high ECM.
"Sea Skimming" good for anti-ship missiles
"IFF Interrogator" means that, it interrogates the targeted aircraft in case of BVR engagements. Not useful for heat-seekers.
"Seeker Uncage" The missile locks onto the target itself
"Seeker Slave" Good for off-boresight missiles, so if you use padlock effectively the missile "tracks" your movement (again useful for heat-seekers) allowing HOBS shots (within parameters)
"Terminal Pop-Up" It'll pop up at the last minute in order to engage targets on the top armor (mainly for effect to me anyways since armor is pretty abstracted within the game IMHO)
"Lofted" means upon launch it'll climb up to a designated angle or height for target engagement.
Best Guidance type is based on what you're trying to do, and all have their advantages and disadvantages. CM Rejection is Countermeasures rejection.
It should be noted a lot of the answers are just simple Google searches, most of the replies were off the top of my head though so I may be a little off.