Here are more of my faves:
Alundra - Not exactly an RPG but it's awesome, kinda similar to Zelda but still fun, and the bosses look cool. And the entering dreams concept and puzzles (despite that they were frustrating) were awesome
Lunar 1 (have barely played Lunar 2 :() - Simple game yet awesome, i don't know why but it was great.
FFIX - One my favorite FF's, next to 10. I kinda felt the "Final Fantasy" theme in this game (i heard this was the maker's favorite FF). Awesome music, awesome towns and really cute chars.
FFVII - I like it but not an extreme fan of it (I kinda think the FFVII original is the best rather than its sequels... then again, i've barely played the sequels).
Secret of Evermore - I enjoyed the alchemy concept and the concept wherein you travel into different places having different era-like environments.
Illusion of Gaia - Great game even though it seemed somewhat short. I was fascinated by the
concept of the ancient wonders such as Mu, Nazca Plains, Tower of Babel, etc.
FFVI - It was big game alright, so many secrets, so much drama, and two worlds. Great story.
Breath of Fire I - Simple RPG, awesome game.
Suikoden 1 - This RPG got me hooked into the entire Suikoden series, the original 108 stars of destiny concept, having your own castle, etc.
Grandia II (not sure) - I really enjoyed it and it was the only RPG that I've finished in the Dreamcast, I enjoyed fighting the
Wild Arms - The story, the ability to summon different golems, the length of the game (especially the secrets).
Chrono Cross - Great story and awesome gameplay. Chrono Series rock!
Xenogears - Great story, music, and places (like Shevat, i <3 Shevat).