The last North American release Nintendo supported on the SNES was a port of Frogger in 1998. This was also the year that the last game in Europe launched for the system: Timon & Pumbaa's Jungle Games. That is funny considering the last European NES game was The Lion King.
Anyway, 1998 was two years after the N64 launched so support wasn’t as widespread as much as for the NES. That is to say, a lot more games came out on that system after the SNES took over. This is the case for Western countries at least, but Japan saw a lot more content on their version of the SNES following the N64. This list then is comprised entirely of Japan-only Super Famicom games.
10 Wizardry I-II-III: Story Of Llylgamyn
Wizardry I-II-III: Story of Llylgamyn released on the SNES on June 1, 1999 in Japan only. This is a re-released set of remakes all of which were Apple II games. The first of which came out in 1981. As such they are fairly archaic even with these enhanced ports. They can also be pretty hard too. For those curious there is a fan path for it in English.
9 Sutte Hakkun
Sutte Hakkun released on the SNES on June 25, 1999 in Japan only. This was a Satellaview game which was both an add-on to the SNES in Japan as well as a downloadable service.
This game in particular is a puzzle platformer. It is unique in that the snowman hero can absorb liquids to make objects appear to then move and or jump on.
8 Power Soukoban
Power Soukoban released on the SNES on June 25, 1999 in Japan only. A Soukoban game, or a Boxxle game, is centered around pushing blocks, boxes, or other objects in order to clear a path to move on. This game is about a demon moving rocks. It’s not bad but getting through the menus can be tricky in Japanese and there doesn’t appear to be a good fan patch out there.
7 Kirby No Kirakira Kizzu
Kirby no Kirakira Kizzu released on the SNES on June 25, 1999 in Japan only. It is a remake of the 1997 Game Boy game, Kirby’s Star Stacker. The West did get that original version but not this which might be because of how late this released. By that point the PS1 and N64 were the dominant consoles for years now. There is a fan patch though to enjoy it in English although as it is a puzzle, there isn't much need for it aside from the menu navigation.
6 Famicom Bunko: Hajimari No Mori
Famicom Bunko: Hajimari no Mori released on the SNES on July 1, 1999 in Japan only. It was released in a similar manor to Satellaview games via a service called Nintendo Power. Not to be confused with the magazine, Nintendo Power was a kiosk set up around Japanese stores where people could plug in blank cartridges and download games. This title in particular was an adventure game which means it is veritably impossible to play without a patch.
5 Columns
Columns released on the SNES on August 1, 1999 in Japan only. This game was first released in 1990 on the Sega Genesis. It is a match-three puzzle game similar to many mobile games today. It received many ports following this original version but this SNES edition was among the last. It was another game released through the Nintendo Power kiosks.
4 Fire Emblem: Thracia 776
Fire Emblem: Thracia 776 released on the SNES on September 1, 1999 in Japan only. It is one of many Fire Emblem games that never came over to the West. Fortunately for diehard fans there is an English fan patch for it. That said it might be worth waiting for an official release. Nintendo did release the first game last year on Switch after three decades so anything is possible. As one can imagine, it plays similarly to the other games.
3 Oekaki Logic 2
Oekaki Logic 2 released on the SNES on November 1, 1999 in Japan only. There was another game in this series which released earlier on June 1, but to save space on here, only one version was be added. It is a spinoff to the Hebereke series, which started as a platformer on the NES in 1991. This title then is a Picross styled puzzle game.
2 Picross NP Vol. 8
Picross NP Vol. 8 released on the SNES on June 1, 2000 in Japan only. As the name might suggest, it too is a a Picross game, but a little more high profile.
Also like Oekaki Logic 2, many more releases proceeded this with the first launching on April 1, 1999. Every entry in this series was about a particular Nintendo character with this focusing on Donkey Kong as the theme. It was also a Nintendo Power flash cart.
1 Metal Slader Glory: Director's Cut
Metal Slader Glory: Director's Cut released on the SNES on November 29, 2000 in Japan only. For some context as this was the last SNES game ever released, the PS2 launched that March with the North American debut happening just a month before this game in October. Nintendo releasing a game that late on a console is staggering. Anyway, it is a remake of a 1991 game of the same name from the NES. That version did get an English fan patch but this remake never did.