Athena - NES. I'm not sure the game had code done by humans.
SSBM - Pretty much any team battle in very hard mode, since your partners were terrible and died almost instantly. Then the computer would come after you in droves and double/triple team you. This wouldn't be so bad if the game was "fair" in terms of amount of damage they receive and you receive, but VH mode pretty much made you weak as shit and any computer opponent massively overpowered.
Sonic Battle - Same as above, especially on Cream's missions. She just f'n sits there and you have to take on two powerful droids with a weak Emerl. *Sigh*
Kingdom Hearts - Having to go all the way around an entire area about 4-5 times in order to move the game along. Also the vines in Tarzan's world were INSANE. I wasted a long time before I realized you can just do the trick in the lagoon area...
Pilotwings 64 - The level where you dive down the side of the mountain on a hang glider.
Vagrant Story - Enemies becoming incredibly strong against any weapon you have, until you get to a new area and can forge new weapons. Also wasting 2 hours on one of the puzzle speed attacks thinking I'd get some sort of reward out of it, when I got shit.
Earthbound - How everyime you moved to a new area, the monsters were WAY too strong, even if you leveled up insanely in the previous areas. Esepcially the damn mall - those cups of hot coffee tore me apart too many times. Also, trying to get the Gutsy Bat in Ness's dream, and how you only had 3 chances of getting it before you had to restart. Plus it was 1 in 128 chance of getting it each time. I'm told you can get it from the mecha krakens in the past, but by then you don't need it anymore...
Yae Ar Kung Fu - My character moves like an old lady.
Street Fighter 1 - See Yae Ar Kung Fu.
Solstice - THE ENTIRE DAMN GAME.
Ecco the Dolphin, any system - I remember it being incredibly hard, haven't tried it in a long while.