Mine is the Mother series because, great story, unique features, and AMAZING soundtrack!

Also, it's overflowed with Beatles references

Mine is still technically releasing (and has been since the mid 90's), and is VERY obscure

I'm a huge fan of the Atelier series from Gust Corporation (localized by NIS America). The games are interesting and funny, but they aren't for everyone, but I'm a huge fan of JRPG's so....

Of note, a new one will be released this year in English (Atelier Totori, the Alchamist of Arland 2 (sequal to last year's Atelier Rorona: the Alchamist of Arland) slated potentially for a September or October release) and, barring the worst in Japan, another one in Japanese (All details confirmed in this weeks Dengeki Magazine, game will be known as Meruru no Atelier: Arland no Renkinjutsushi 3 in Japanese, slated for release June 26th).

would pokemon count?

I would say it does since it is an RPG from the mid 90's lol. You have to figure most of the titles noted here will be from that timeframe, considering that's when most of the mainstream RPG's either started, or made their debut in English (Unless of course, it's my favorite, which debuted in 1997, but didn't get an English release until 2005 . Good thing I ordered those Japanese PS1 and PS2's so I could play the imports ).

Does Paper Mario count? Technically the first game was released in 2000.

Final Fantasy 7 for PS1. That was pure epicness. Other than that, I am not a huge fan of FF.
I bet TBY will say Fire Emblem xD

Pokemon would count and Paper Mario would to since Super Mario RPG is kind of a prequel to Paper Mario.