The Atari 7800 was clearly underappreciated because it was actually the last good Atari console before the infamous Atari Jaguar, and was the best attempt by Atari to win back their customers after the North American Video Game Crash of 1983. Therefore, this underrated console from Atari would be a respectable find from the bargain bin, if they can be found in the bargain bin that is.
Who would have thought the original arcade version of Mortal Kombat would have gotten the Plug & Play treatment? Surely there are some people who would have tried to lay their hands on this piece of video game history if Mortal Kombat was not banned in whichever country they come from...
If you dislike the North American box art for Karnaaj Rally to the point you chose not to pick up a copy of the game, then you have not heard about the European box art for Karnaaj Rally, which was actually good box art design. Karnaaj Rally is actually a decent racing game for the Game Boy Advance. Therefore, ignore the awful box art and go get a copy of Karnaaj Rally from the bargain bin if you regretted your decision to give Karnaaj Rally a miss due to the bad box art.
Another underappreciated console that can be found in the bargain bin as a rare find is the PlayStation Vita. This was a handheld that cost more than the Nintendo 3DS even when these two handhelds had similar battery life. No wonder the 3DS outsold the Vita by a long shot. Gamers are becoming more thrifty as the effects of the 2008 downturn lingers on after 15 years.
PES 2014 was officially confirmed to be the last game released for the PlayStation 2, so you can expect this game to be a rare find in the bargain bin.
Redesigned versions of great consoles often get released near the start of the twilight years, and the original PlayStation was no exception. The PS One was released in 2000, the same year Sony released the Playstation 2. Therefore, expect to find a PS One in the bargain bin, although such an item will be a rarity.
Speaking of bargain bin rarities, Compile's last game, Pochi and Nyaa, is an uncommon PlayStation 2 game that can be found in the bargain bin. But it is not easy to find the PS2 version of Pochi and Nyaa in the Japanese video game store bargain bin because Pochi and Nyaa was Compile's very last game before they closed their doors for good.