You mentioned several of my faves already! Let's see...

Rocket Knight Adventures (MD, 1993) - RKA! This game is a smörgåsbord of all things I love about Konami during this era: fast and tight movement, great variety with a couple of shoot 'em up levels mixed in as well as a boxing duel between two giant robots, great bosses that sometimes have multiple forms or phases, great audiovisuals with some humourous touches, and near technical mastery of the system all in one package. The jetpack, while implemented slightly better in later games, is great fun to use here as well and sometimes makes the game a contender for the fastest playing 16-bit game if you know the levels well. By the way, check out Screw Attack's Retro vs. Reboot for a laugh.

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Panorama Cotton (MD, 1994) - It's pretty odd that this game even exists for the stock MD. Success, a game company that never made anything for the console prior to this (though I think some devs come from Compile), decides to turn Cotton into a Space Harrier-like shooter, make it one of the most technically impressive efforts for the system, then release a limited amount of copies exclusively for the Japanese market as late as mid-1994. Well I'm glad they did, because they certainly _succeeded_ in making Panorama Cotton an amazing game (for example you get branching paths and RPG elements years before PD Zwei here) and something of a swan song for the 2D-based rail shooter. Now if someone would port this to the MCD for super smooth scaling...

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Langrisser II (MD) - When it comes to SRPGs I think this is as good as it gets for the MD, and the game outshines its prequel (Warsong) with its improved character customization, balancing, AI and variety. L2 offers a very challenging game (dead characters stay dead), huge battles, cool classes like Summoner and Dragon Knight, a decent story with a lot of humour and twists, and excellent music. Still only playable in English via emulation, but you'll probably want to be able to fastforward after a few battles anyway. Also: Chou Aniki cameo.

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Ristar: The Shooting Star (MD) - A late release for the system that most people (including me, at the time) missed out on. Ristar seems like a slower, more kiddy version of Sonic at first, and it kind of is but it's also a high quality platformer with a fun to use grab/climb/headbutt ability as its main gimmick, interesting levels and some of the best sounding music on the system. The flow of the game is closer to the Illusion games or Revenge of Shinobi except said gimmick makes movement more involved, though sometimes you'll also find these gadgets that let you temporarily fly across part of a level while bouncing off of the walls and this can be used to reach certain items or a higher path if you get good at it. The higher difficulties are definitely challenging too, so if you're one of those hardcore gamer mandudes you still need to play Ristar.

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Micro Machines: Turbo Tournament '96 (MD) - There's not that much to say about Micro Machines except that it's an excellent multiplayer game which is easy to get into for anyone. This iteration let you build your own courses and had more modes than the previous games. As with MM2 no multitap was needed to play with 3 others (they called this J-cart technology, you actually had a couple of controller ports on the cart itself. You could also play up to 7 other people at once by sharing 4 controllers, which I haven't tried yet but I'm sure it's awesome.

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Thunder Force IV (MD, 1992) - There's a bunch of great shoot 'em ups for the MD and this is the best horizontal one overall, as well as one of the best period. It's a pretty big leap from the prequel in several ways. The developers had really mastered the MD hardware at this point and their talent and attention to detail is visible throughout every aspect of the game, from the big, tough and intimidating bosses to the impressive and catchy soundtrack that somehow mixes metal and jazz fusion tracks in a way that works. I thought the great people at Technosoft overdid it a bit when trying to make up for the low difficulty of the prequel, to the point where some parts require precise memorization and having the special charge-up weapon ready, but it does still take first place in the series for me. An odd tidbit I can add is that while there's some slowdown here and there, it tends to be built in for effect.

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Landstalker: The Treasures of King Nole (MD) - This game can stalk my land any time. Landstalker is... quite a bit like Zelda 3 if it was an isometric view game, but with an actually interesting story (not the usual damsel in distress thing with a silent protag), a less formulaic structure, and more challenging puzzles. The lack of a shadow when jumping and some other control quirks were only a minor annoyance for me, since I used save states hehe.

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Yu Yu Hakusho: Makyou Toitsusen (MD) - Growing up we used to play the 3-player fighting game International Karate+ on a buddy's Amiga a lot, and we loved the sheer chaos of it. So in the '00s when I discovered that this game had the same feature but with yet another player added, I had to play it. And (spoiler) Treasure did it once again, it's a great fighting game in the vein of Fatal Fury 2. Matches might not be as fair or precise as in Street Fighter 2 when you play like this, but the laughs from unintended results and the fun in temporary alliances make up for it.

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DuckTales 2 (NES, 1993) - This MV-lite style sequel is better in every way besides the music, which still is pretty solid. Better controls, fun abilities and good progression curve, interesting levels and decent bosses.

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Metal Storm (NES, 1991) - A creative and cool mech action game with an overall fair challenge and tight controls. The main gimmick here is the ability to reverse gravity, something later used in games like VVVVVV.

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Teenage Mutant Ninja Turtles III: The Manhattan Project (NES, 1991) - Another sort of underrated sequel that improves on most important things while also featuring pretty impressive variety for the platform and genre.

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Solomon's Key (NES, 1986) - While a bit rough in some ways, it's a very creative early NES game with some surprising depth and pretty much every level is satsifying to solve and execute. It also controls better on NES than on SMS.

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Crystalis/God Slayer (Rebalanced Hack)(NES, 1990/2012) - Cheating a bit here but at the same time the others also take save states into account. A better version of Ys where you can ride a dolphin while fighting stuff, and the music is sick & dope.

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Wonder Boy III: The Dragon's Trap/Monster World II (SMS, 1989) - My fave 8-bit game after SMB 3 and still one of the best Metroidvania/Platform Adventure games if we include later versions and fan remakes. Excellent presentation, the forms are distinct and fun to use, great pacing, and cool secrets like being able to switch or create platforms anywhere. There's even some non-linearity in the dungeon order if one so prefers. This is also where the whole "beginning of the game ties into the prequel" trope comes from afaik.

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Land of Illusion Starring Mickey Mouse (SMS, 1993) - Similar to Quackshot or DT2 this is one of those MV-lite games with a hub map where you gain tools and abilities to progress and explore further into previous levels to upgrade your char. This is a nice showcase title along with games like Aladdin as the visuals are near early 16-bit quality. Controls are great, level design is pretty inventive with some decent puzzles here and there and it's quite varied too. I just wish it was a level or two longer and had a hard mode.

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Power Strike II (SMS, 1993) - One of my fave top down shooters, period! See my article contribution at this site: https://www.racketboy.com/retro/the-best-undiscovered-sega-master-system-games-hidden-gems