Best... Well, it was probably too long since I played it for me to make a qualified choice, but now that I've seen it in writing, I actually thought that the return to Garden after Missile Base (NORG/Cid? Evacuation/gallivanting in the basement) was pretty intense.
Worst: As much of an anticlimax as it was when I finally came face to face with Ultimecia (we... got off on the wrong foot, ya), I think the last Laguna-sequence bugged me the most, actually.