So The Orange Box is a port, hey? The reality is that the situation isn't black or white but a sliding scale.
HL2, Episode 1, Episode 2, and Portal are all games that would be considered console games by today's standards. Console games have advanced quite a bit in the past few years and you may not realize that the controls you use in those games are simple enough to be called console configs by today's standards. Playing through episode 2 didn't feel any different than playing HL2 and ep1 on my PC. The experience was the same.
The experience for TF2 was significantly different, for a variety of reasons, so I'd say that is a game that takes better advantage of the PC's features.
And Bioshock was absolutely designed with a console player in mind. Console games don't have to be bad games, many are exceptionally good. CoD4 is still one of my favorite games. Bioshock was friggin brilliant. But most games that are available on the PC and consoles are not better games on the PC. Most are the same game completely.
World in conflict is a good example of a PC game that I believe is designed for a console. The basic controls have you moving the camera with set of keys, while controlling the direction it's point with the other (mouse). It's a setup that would map EXTREMELY well on 2 analog sticks. I don't see this as a bad game, I see this as a good step towards making games completely cross platform so pc users can battle console users and have the same exprience. I decided against buying this game because the actual gameplay was not very complex. You had a limited selection of units and I felt a PC user could manage a lot more game, but they were trying to keep the game simple enough that a console user could play it just as effectively.
I guess what I'm saying is that it's extremely unusual for companies making cross platform games, pc/console, to really take advantage of the PC. I think people are happy to see these Big budget AAA titles available on the PC's but it's a step back in time. Eventually things will advance back to where we see current PC games but it's going to take some time.
Heck just playing Supreme Commander and CoH in the past few days have made me appreciate how much more you can do in a game on a PC. Most games don't bother building those features into their games because console players won't ever benefit from them.