If you are looking for a realistic modern-era FPS, these are my personal choices:
-Operation Flashpoint: really good, although the graphics now look somewhat outdated (being a 2.5 years old game), but the gameplay is at the same time serious and fun.
-Ghost Recon: good graphics, good and realistic missions with a nice geo-political setting. The only thing I don't like is you can't control your team as much I would like to do. And some people don't like the fact that you don't see your weapon, personally it did not bothered me.
-America's Army: this one is surprisingly good, and besides, it's completely free (well, not really, since American taxpayers paid for it, thanks to all of you!)
Although not a strict FPS, I am impatiently awaiting Full Spectrum Warrior later this year:
http://www.fullspectrumwarrior.com/
This game has been developed initially for the US Army to teach MOUT techniques to soldiers. They are making a game out of it. It seems very realistic and fun to play.
For WWII, Call of Duty reigns as King, although its main quality (heavily scripted game that makes you feel like you were there) is also its main weakness: once you have played once, there is not much incentive in playing it again.
Medal of Honor was good, but it's getting old.
Watch out for this one though, it sounds awesome:
Brothers in Arms. Other info is also available here:
http://www.gamespot.com/pc/action/brothersinarms/index.html
This is a realistic tactical shooter based on a true story (much inspired from the Brothers In Arms serie of Spielberg). As squad lead, you will be able to give orders to each of your AI-controlled team mates, and you will have to use realistic tactics. There is no blasting your way in this game. This one's a must buy for me.