Raiden.
Haha, just kidding guys. If Raiden was included, I would probably chose him -- although I am not too sure yet. I like the dude, and I like MGR, but I couldn't call that game "development" for him as a character. ( I hope MGR2 fixes dat ****)
But without digressing too much, I'll be straightforward and say it's Solid Snake I prefer.
It may have something to do with Snake being the first Metal Gear Solid character I got to meet, but to me, Snake, as a clone, feels more relatable and alive than Big Boss, don't ask me how, but the clone wins there.
Besides that, I only really liked him as Naked Snake, in MGS3, and even there, he spent a lot of his time angsting about his cherished Boss when it came to it and didn't really accomplish an exceptional lot.
I like Big Boss too, but I gotta be honest and give my vote to the Solidmeister.