HTC

I prefer HTC already. Sense is, in my opinion, the best UI on the market right now. As for the Samsungs, I think they have the best hardware on the market, unfortunately they preload way too much garbage onto most of their phones. I have heard great things about the Nexus S (Samsung phone without the bloat) and would probably go that route if the Thunderbolt werent right around the corner.

Long story short, I'd take HTC phones right out of the box. Rooting a Samsung probably gives you the best phone for your money though.