Well, let's see...
Super Mario Bros 2
This one was fun and while it wasn't my favorite of the NES Mario games, it was incredibly fun but wasn't received very well and still isn't received very well.
Zelda II: The Adventure of Link
Again, not received very well and often looked down upon as "crap" in the series, but I like it. A lot, as a matter of fact.
Super Mario Sunshine
It was critisized a ton for having voice acted cutscenes and FLUDD and all that, and while it wasn't my favorite 3D Mario game, I definately enjoyed it a lot.
Pokemon Mystery Dungeon
Just Pokemon Mystery Dungeon. For some odd reason or another, it gets a lot of hate and I have no clue why. Sure it's not the same epic type of game we all know and love, but it stays true to the original Pokemon design while bringing fun new twists. Say what you will about the PMD games, but there is no denying that it has the BEST plot in any Pokemon game, spin off or not. Any game that can make me cry (thank you, EoS/EoT/EoD, for one of the saddest endings in a video game ever) automatically has done the plot incredibly
Also, yeah the gameplay might not be in the same format. Sure, you're not some random ten year old going around catching wild animals and battling them. Sure you don't go around collecting gym badges to challenge powerful trainers known as the Elite Four. Sure you don't go into grass and have random encounters. Mystery Dungeon actually kept alot of the concepts for the original GB/GBC/GBA/DS RPG's while providing new twists. There was actually turn based combat in the games. You move, your partners move, then your foes move. And really, the only difference between combat in the classic main series games and the PMD series is that you don't go to some fancy screen to battle one at a time and there aren't any random encounters. You explore through dungeons, the layout and items of which changing with each visit (which is an amazing concept), and as you go through the dungeon, you encounter Pokemon with whom you just battle almost as though it were Zelda with a menu for attacks.
Also, the music is outstanding. Just listen to some songs like PMD2 Boss Theme
, PMD2 Opening Theme
, Wigglytuff's Theme
, PMD2 Time Gears
, PMD2 Anxiety
, PMD2 Strange Happenings
, PMD2 Monster House
, PMD1 Stop Thief
, PMD1 Sky Tower
, and a ton of other songs that I'm not going to list for the sake of not making this whole post just links to epic songs from the PMD series. PMD does NOT deserve all the hate it gets. Show me the love!
Sure, it's different from the main series, but as was proved with just about every other game on this list, being different doesn't diminish the value of a game.
It had the same sort of gameplay the usual Pokemon had, but with a twist: you liberated Pokemon used for evil purposes from criminals instead of capturing wild Pokemon from the wild. Instead of beating up Cipher/Team Snagem, you stole their Shadow Pokemon (which brought with them a cool new mechanic with them) and saved them.
The plot is also somewhat derived from the main series games, but the gym quest was completely cut out (unless you count that one practice gym, but you don't get a badge from it). Again, just being different doesn't diminish the quality of a game.
Pokemon XD Gales of Darkness
See the section of my post about Pokemon Colosseum, as it's just a copy/paste deal with these two games.