MGS3
The best story ever, bosses you almost don't want to kill (especially the end. He's so awesome. I didn't bother saying The Boss, because its obvious). It also was very well made with the "go get sum food" system and wounds system, upped the realism a big notch. Very good
About Raiden... well, mgs2 had a kinda realistic story (except a bullet dodger, a vampire, a fat guy on rollerblades and such) but raiden blew it...
MGS4
I have it, and have completed it.
*WARNING; SPOILERS AT THE END OF THIS POST aftetr the big empty space*
Well, it sure has insane graphics. And the story with an old snake is very, very well made. The system have changed very much, and uses the system you might remember from MGO beta. The octocamo is quite awesome, so are the "Beauty and the beast" unit (like cobra unit from MGS3).
But it's strongest card are the almost over-epic ending and the nostalgia (more info in spoilers)
ATM i like MGS4 best, but i think its kinda a tie between MGS3 and MGS4

IM SERIOUS IT WILL BE BIG SPOILERS
*SPOILERS*
The so called over epic ending is divided into two.
First, you encounter a LONG corridor which is influenced with microwawes. You start walking it, pressing triangle wildly, then drop to your knees, before crawling on your belly. You can FEEL snakes pain.
The other is a fistfight with Liquid Ocelot, with a fighting system almost awesome. You do a CQC grab, and throw him, BUT you presss triagnle and mount him and smack him, or smack him into the wall and such.
And Vamp, Raiden, Big Boss (! ending cinematic) anr more returns...