GameCube.

It had amazing games and fixed like... 75% of the problem of media storage and crap controller that plagued the N64.

It should have sold more than its predecessor, at least.

I was thinking Gamecube, but that has gotten a lot of love in recent years. Ill go with the Master System. Such a gem of a console.

The most underrated game system is the PC, especially on this site

PS Vita. The system itself is probably the best portable machine ever created. It was powerful, the screen was amazing, it had dual analog sticks... and it was still portable enough to fit it in most pockets.

It also had plenty of great games if you knew where to search for them. And Remote Play is an amazing option that doesn't get mentioned enough.

Of course, lack of strong first party support, memory cards and not being able to keep your save files when deleting a digital game among other things, keep the system from the big names on the industry... but its good things best the bad things, making the Vita an overall great console.

The Vita is easily the most underrated. Spent so many great hours with that thing.

Sega Master System

Better graphics than NES and some really good games RIP Alex Kidd and Phantasy Star

Xbox 360.

Massive library of stellar games, very comfortable controller, beastly powerful for its time, had the best (console) version of most 7th gen multiplats.

Gets a lot of flak for the failure rate of early models, but this was fixed with the slim. 

The Amiga what a great gaming machine.

This is the only system anyone has mentioned in this thread that really qualifies as underated. There's all kinds of love shown to GameCube, Vita, and OGXB. But Master System really has been overlooked, and was overlooked in much of the world even when it was current.  It was better than the NES in many ways, but it was missing a Mario level iconic character. And, consequently, was overshadowed by it's weaker competitor.

Edit to add:. Someone mentioned the Sega Saturn as well, which certainly qualifies as underated.