I just got Tekken 5 the other day and I was blown away by the graphics on this baby, but I think I still prefer Virtua Fighter 4.
I like VF4 because the controls are simple (just puch, kick and guard) and intuitive while simultaneously being very deep (guard-throws for instance).
I also like how balanced the characters in VF4 are, compared to Tekken which has lots more characters, but has quite a few that are very similar. VF4's characters almost always have their own unique moves and combos, which makes playing them a more in-depth experience.
Tekken also seems to allow more room for button-mashers to do well, while VF tends to reward experience, which I like. There's nothing like the shame of being destroyed by a button-masher, or the glory of putting one down with a perfect.
So what's your favourite one on one fighter, and why?