VII for gameplay and world
Serpent Isle for story (although Pagan seemed to have a good story, it messed too much up)
If Serpent Isle were not quite so rigidly linear (mostly understandable due to the story) and the team had not been rushed by EA into ruining much of the late game, it would definitely be my favorite.
VI was pretty awesome too, but both parts of VII wers just so much more immersive. The Underworlds were incredible, especially part II.
I have yet to play a game that makes me feel like I am as much a part of the world as Ultima VII. The ability to take all types of food, plates, silverware, clothes, underwear, and many other items from every single home in every town was amazing. You had the ability to steal literally anything that was not bolted down. You could bake bread, spin thread, own various boats, and even play Sherlock Holmes in the various mysteries. The story about the brotherhood was far more complex than it seemed and the guardian was quite sinister.
The world was MASSIVE and full of fascinating locations, and the magic weapons you found later in the game were usually more fun and clever than overpowered (although the Hoe of Destruction was perhaps too strong considering that the door to its shed could simply be blown open with a powder keg instead of searching for the key).
The party members and NPCs may not have had the AI interaction of Fable, but the scripted events led to many opportunities for characters to like or hate you. The Avatar museum was qute an experience too and noone can deny the fun of raiding pirate forts.
Serpent Isle was much more dramatic, but it reduced many of these elements for the more complex story as well as the stric trelease schedule of EA.
The two also run even better than before with Exult. Ultima VII is still my favorite PC RPG.