Radiant Silvergun is at the top of my list, along with these:

Cyberbots: Capcom's robot-based fighter never got beyond location testing in American arcades, but the Saturn version does a great job of recreating the coin-op original. Great mech and character designs, loose-yet-enjoyable gameplay, and an actual story make this an unjustly obscure piece of Capcom history.

Policenauts: The follow-up to the digital comic classic Snatcher, it's perhaps more text-intensive than any other recommended import, but no game provides a better reason to learn Japanese.

Princess Crown: It may well be the single most gorgeous 2-D game I've ever seen, but there's an excellent action/RPG under the pretty hand-drawn art.

Tengai Makyo IV: As an RPG, it's decent, but the real charm of this one lies in its setting, a deliberately warped take on 19th century America. Nothing beats a Japanese actor trying to say "Alaska" in a Southern accent.

Sakura Wars: Part strategy/RPG, part dating simulator, and part anime series, the original SW is far more than the sum of its parts. The tactical portions are fun, the storyline's a interesting tale framed by a steampunk vision of early 20th century Japan, and the "dating" parts are tasteful and surprisingly fun.

Keio Yu Gekitai: A fun and uniquely Japanese platformer, this wasn't translated because American companies were dumb. Or perhaps because the game stars a girl in a bunny-waitress getup and would have sold all of twelve copies in the U.S. Take your pick.

Others: Vampire Savior, Soukyugurentai, Dodonpachi, Cotton 2 and Boomerang, X-Men vs. Street Fighter, and Batsugun.