I voted Two Thrones. I love the entire Sands of time story, but this gave the closure I needed. Story means a great deal to me. And I have to disagree with Keksus on the gameplay: The quicktime events were an option, not mandatory until boss fights. besides, I loved the stealth feature, a great change of pace from the hack and slash of WW and SoT.
But every time I want to play this one, I like to hear the whole story, so I play all three games.
I think gameplay wise, PoP 2008 is better than WW, but not as good as the other 2. Story wise, it's incomplete, so I can't fully appreciate it yet. (Classic is just a time wasting activity, I just play it when I don't have time to immerse myself. No real story and somewhat frustrating control at times.)