I have a few more to offer.
Gauntlet (the new one) offers a nice challenge that stands out it a weird manner of speaking.
FTL is surprisingly challenging due to the random events.
Any of the DOOM games with the Brutal Doom mod attached. Adds a nice twist to the old series, and playing on black metal is a pain in the ass (I would know, I beat it).
Also Osu! because I'm not Asian.
There are more I can list. I know you asked for the "hardest Video game" I've played, but its hard to pick just one out. The games I play have difficulty in respective areas.
Gauntlet is enemy management, FTL is a highly strategical game, and Brutal Doom is a fast pace shooter. DMC 3, in all fairness, should be taken off the list. And that is only because dante must die is not challenging just from a base perspective, you cant even get that mode without playing the game, but its a skill cap difficulty.
If I wanted to look at other games I found difficult to worth mentioning, I'd go back to old ps1ish era of games. Frogger sticks out as a very difficult arcade style difficulty. Where Final fantasy tactics would likely be the most strategical challenging game.
With all that being said, can you really say a difficult game has a "base game difficulty?" All of them require practice and acquired "skill" to play efficiently. I'm way better at Brutal doom for having beat the hardest difficulty.
Anyway, just some general thoughts.
