Was there a thread about this? Google-fu isn't working for me.
In Ange Vierge series (12 episodes anime) I spotted 2 different classic consoles.
First up is a scanning device that looks suspiciously like Sega Game Gear with a TV adapter:
Second one looks suspiciously like a Dreamcast:
In the anime Asobi ni Iku Yo! series there's a few consoles in a game shop including PC-FX, Dreamcast with too many ports, spice orange Gamecube, and I think a CDi on steroid?
Hunter x Hunter had a few game consoles but none resembled known consoles although the main console used in the Greed Island and Yorktown arc was interesting. Dual drive, 2 memory ports, and 4 controllers ports that looks like standard PSX. The memory card also looked like standard PSX and could be expanded to 8 memory slots per slot.
Monster Rancher featured PSX.
Baka to Test had Famicom (classic)
Ah My Goddess has a lot of consoles and it looks like hacker heaven! Famicom, SFC, PC Engine, Genesis, PSX, and a few more unidentified consoles.