Sho Nuff wins the thread, no contest.
Have sold off a lot of the 'rare' and pricier stuff over the years, but here's some things that stand out off the top of my head. Need to look through my collection.
-Famicom Gameboy Micro. Still have everything for it including the box and it's in pristine condition. Might end up selling this off once that Analog Gameboy clone comes out.
-Street Fighter III Third Strike Limited Edition for PS2. IIRC I got this when I was walking around Akiba with Bebpo way back in 2004, lol.
-Bayonetta Climax Edition for Switch- this is the only way to get a physical copy of Bayonetta 1 on the console. The price just keeps on going up.
-Senran Kagura 'NyuuNyuu' DX box sets- have the "complete set" of these for Senran Shinovi Versus, Estival Versus (Vita and PS4), and SK2. The two Estival games' boxes go together to make one long box artwork and each set comes with little chibi figurines of all the characters. Some of these are pretty hard to find now, but at one point the DX box for Senran Kagura 2 was in so little demand that you could get it for like thirty bucks off Amazon, lol. I also have a Peach Beach Splash poster signed by series producer Kenichiro
"tits are life, ass is hometown" Takaki.
-Samurai Spirits (PS4) NeoGeo AES Box-style alternate cover version from the SNK Samurai Spirits Akihabara pop-up shop. Dunno if this is even remotely "rare" now since I found out there's like four different box types and an extremely limited American production run (like 200 copies), sold only at a tournament, is also out there. This shop is gone and they now have (or had) a pop-up shop dedicated to Mai Shiranui to replace it. Also now have an AES-style Switch version and pre-ordered a European production version of the game, also in an AES box, that will come with a physical version of the SS!2 NeoGeo Pocket port of the game. Love this AES box stuff.
-Ninja JaJamaru Collection (Utage Set LE)- not sure if this even counts- it's Japanese, but the Utage Set LE was a crazy limited edition release from Dispatch games with only 200 copies available, however I'm not sure if that meant "200 copies available from Dispatch" or "200 copies total."