The first two Dragon Warrior Monster games I'd consider the best ones in the series. The Joker games are also good, but not as good. Dragon Quest Monsters 3 Caravan Heart sucks ass.
In the original game you could have a monster that, potentially, has access to every ability in the game. In Dragon Warrior Monsters 2, you can now only have access to eight skills at a time. Kind of sucks, but eight is enough. The original has randomized maps depending on the gate that you go to, while Dragon Warrior Monsters 2 has your regular worlds that are the same each and every time you go to them, but literally an infinite of randomized maps depending on the key combination. You could have two keys with the exact same name and it could be a totally different maps.
I like the GB ones the best because everything is much quicker and a larger variety of areas and monsters.