For me it has to be Metal Gear Solid for the Playstation as it is also my favorite game period. But I love them all. Snake eater is probably my least favorite, it is the only one so far I have only played once.
I typically don't watch a lot of anime but a friend suggested I watch Fullmetal Alchemist and through coincidence I received the complete set of it for Christmas from my mum and sister (they think playing games automatically means I am into that stuff :-I. Anyway I recently finally started to watch it and I don't mind it that at all so I would probably go with that. But the only other series I have are Samurai Champloo and all the Dragonball stuff and a smattering of feature films so I don't have a lot to draw on. I tend to enjoy the Studio Ghibli stuff I have watched as well.