1) Warp – basically FTL travel in normal space since the ship can interact with things in normal space.  Star Trek is the only show I know of that uses this method, though the U.S.S. Merimack book series by R. M. Meluch does it, too.

2) Hyperspace – the title refers to the most common name for it, but its basically any method in which the ship goes into “other space”, travels for a bit, and then comes back into normal space.  Star Wars, Babylon 5, and Andromeda all made use of this system.

3) Jump – this is usually explained by folding space, but basically refers to instantaneous travel  between origin and destination.  Starblazers, Macross, and the new Battlestar Galactica all used this method.  Stargate and Buck Rogers in the 25th Century used a variant known as the Gate (although Stargate would be a slow Gate since it wasn’t an instantaneous trip).

If there is true normal-space FTL, then a proper galactic coordinate system would be important. I would follow ST and put the origin at the galactic center–unless you are always in this sytem, it is just simpler that way than trying to orient yourself to Sol (and, unlike earth, the galactic center is exactly in the galactic plane, simplifying your z). I am partial to the idea of semi-polar coordinates–a θ/r system for orientation on the galactic plane and an absolute h. I can see the advantages of a Cartesian system for calculating distance, but a computer could handle either just fine and I think the polar or cylindrical more useful for orientation.