This is for talking about both main and side games, but what games would you say you really enjoy but seem to be underappreciated by the "mainstream" Pokemon community?
For me the whole 3rd generation of main games seems to fall in this category for one reason or another...
Ruby/Sapphire got a lot of heat for lack of backward compatibility with the previous games and what initially seemed to be no way to get some of our favorite old Pokemon (in many ways you could say this was the series' first "reboot" even before Black/White), but it introduced so many awesome game mechanics and even without online play, it had some of my favorite use of interactive connectivity with the secret bases and the ability to sync up with your friends and have their bases and parties in your game to battle against.
FireRed/LeafGreen were also some of my favorite games in the series but because they were remakes, especially of the "golden children" of the series, maybe they didn't come off as appreciated as expected. I also wonder if maybe Nintendo didn't give them as much consideration since the main thing that really made them stand out in comparison with RBY, the Sevii Islands, are nonexistant in HeartGold/SoulSilver.
Colosseum/XD have to take the cake as far as underappreciated games go in my book, at least for the main series. Lots of people have wondered what a Pokemon RPG would be like on a console, and even though it came in a slightly different package then the handheld games (no wild Pokemon in Colosseum and only a few for XD because of the emphasis on Shadow Pokemon), I think both of these games delivered in a big way. I found myself very much engrossed by the concept of a tougher storyline and the Shadow Pokemon, even though I only rented Colosseum and never got to play XD. Unfortunately, even Bulbapedia refers to them as side games and doesn't even consider them a part of the main series, despite the fact that it plays essentially the same as the handheld games! What seems to be the most disappointing is that probably the ones who appreciated this game the least are Nintendo, since they went back to the Stadium gameplay in PBR when the Wii and later gens would have made for even more amazing adventures.
I guess even Emerald counts too because people seem to see "3rd game" as merely an expansion pack. Emerald seems to do this more than Yellow (with your Pikachu partner) and Crystal (1st time playing as a female character), only really adding the Battle Frontier, slightly improved fonts, and green clothes.
So that's my rant, but I know I'm not the only one. I would love to hear the gems from y'all's collections. Maybe someone will bring up something obscure like the Pokemon mini or the Pokemon Project Studio. Other forms of media besides video games are accepted too, like maybe a TCG expansion that didn't get a lot of publicity.