Well, not technically through hacking games. But I have found a few interesting things when trying to data mine them outside of TCRF (via a tile editor), or when messing around with codes.
For example, Wario Land 4 has an unused animation for when you kill the seagull in the Wario Hop. As far as I know, this was never used in the actual game, since you can't jump high enough to interact with it.
It also has various beta tiles found underneath the ground in levels too. And there's a room past the far right wall in Palm Tree Paradise with a diamond and some enemies in too. Found that one years before TCRF or other sites about 'unused content' were ever established.
I also found a bunch of unused songs in Luigi's Mansion 2, though I was looking to post the soundtrack in high quality rather than actually mod the game. I eventually registered and (with the help of another member there) posted the songs and stuff on the wiki in the right location.