I can't really speak for MG and MG2, because I have yet to complete those. But, by game: In MGS1, I found Sniper Wolf to be the hardest, though only because the PSG1 is so annoying to handle. The second battle can be exploited using the Nikita, but still. In MGS2, I used to find the Harrier the hardest, since I didn't know how to dodge the carpet bomb attack. Now, I don't know. The Metal Gear Rays I guess. In MGS3, I didn't really find any of the bosses hard, but The Boss was probably the hardest. In MGS4, once again, none of them are really hard. The Laughing Octopus fight drags on a bit, so I guess I'll go with that. In Portable Ops, the final boss was probably the hardest. As for Peace Walker, in Main Ops, the second Peace Walker battle gave me trouble on my first time, but now I just find it time consuming. The real hard bosses are the mechs, AIs or monsters in Extra Ops. And in Rising, I had the most difficulty with Metal Gear Excelsus.