I enjoyed all three POP games immensely, with Two Thrones being the overall "best" and Warrior Within being the "worst". But that doesn't mean much, because all three games are great in their own right.
Sands of Time was a great introductory game to the revitalization of the series, but after playing WW and TT it seems overly tame and repetitive, especially with the battles and formulaic design (Solve huge puzzle, fight tons of dudes, do crazy platforming, fight tons of dudes, save. Repeat.). However, it's a game that I can go back to and play again after playing the other two in the series, and that shows its value in my eyes.
Warrior Within's music is awesome, in and out of the game. I have the OST and enjoy it a lot; especially the "generic" butt-rock. If I were chased by the Dahaka for seven years I'd be pretty pissed off about it, too, so I can see the Prince's "dark" side being an important part of the game. What I did not like about WW was the backtracking. If it were a solid adventure like SOT or TT, I would have liked it a lot more. However, it was still a lot of fun and to this day is more enjoyable than more than 90% of the action games that are out there.
Two Thrones was the best of the three, IMO, because it took the best parts of SOT and WW and threw in some new gameplay mechanics to make the best action title of the year. Maybe it's just me, but TT was way more fun than God of War. The duality of the Prince and Dark Prince is perfectly implimented, from the differing play styles to their attitudes and overall appearances. TT welcomed back linearity, which is a strong point in this series. Great music too, although there is no butt-rock to be found.
I just beat TT last month, but I want to go back and play through the Trilogy again sometime soon.