well since most RPGs are text based you might want to stick to games like Tales of Hearts or Blood of Bahamut since you don't need to follow the story to play all the way through(its good to know the story but not necessary)
Choushoujuu Mecha MG is one of those games that should have been ported how it wasn't I have no clue but you'll probably never see a better mech game than this sense they turn them all into shooters now -_-
only catch is when you equip new parts it helps to be able to read but Game Faq has a translation guide for that, so other than that you can get by with out being able to read..
Utacchi is a good rhythm game, especially if you're into JPOP/Anime, as some of the songs there are directly from the anime themselves.
Culdcept DS also is a great boardgame/cardgame hybrid, with online features, that are currently japanese only, but they have a great translation patch here that is almost done for the most part. once you get the gist of the game, it's quite addicting.
Some of the not so popular japanese games i've played: Prince of tennis series (Tennis no Ouji-Sama 2005 - Crystal Drive)
Quite liked this tennis game since i also like the anime. Game has some special tennis moves thats cool
Gundam Mahjong DS - Oyaji ni mo Agararekotonai-noni
I was looking for a mahjong game.. though i dont really know how it works, its kinda fun.
Crayon Shin-Chan - Arashi o Yobu - Nendororo n Daihenshin
Crayon shin chan sidescroller. Its kinda like a mario style game. It has some weird/hilarious game mechanics
Taiko no tatsujin series (drum master)
This should be popular, its one of my favs