here's a list of references that come to my mind
**Megaman 3** in Snakeman's level there are enemiees that very closely resemble bullet bills
**Metal Gear Solid Twin Snakes** when you first make it to Otacon after finishing the boss fight with Gray Fox you can see that Otacon has a Mario and a Yoshi figure on one of the monitors, if you shoot the Mario figure you hear the 1-up chime, if you shoot Yoshi you get the famous Yoshi cheer, another reference is before the Psycho Mantis fight, he reads Snake's mind and one of the things he says is "i see you've been playing Super Mario Sunshine"
**F-Zero** in the series the character Mr. EAD has a face that's closely designed after Mario, while you may say it's a coincidence, you can tell it's intentional because if you look at his belt buckle, it's the star from the Mario series complete with it's eyes
**Banjo Tooie** i can't remember the entire part of the scene but there's a Mario reference involved, if you talk to the clauged toilet guy at Grunty Industries Kazooie will tell the toilet guy to call Mario