Okay, here's my approximate ranking of both Heisei and Millennium films, excluding 1984's The Return of Godzilla since I haven't seen it.
1. Godzilla vs. Mechagodzilla II (Heisei): One of the most thoughtful, philosophical films in the series, with good character work, good action, and great music.
2. Godzilla, Mothra, King Ghidorah: Giant Monsters All-out Attack (Millennium): Also known as GMK. Another film with a strong philosophical bent, and the darkest, most powerfully anti-war Godzilla film since the 1954 original. Pretty bad Godzilla costume, though.
3. Godzilla vs. Destoroyah (H): Climax of the Heisei series and in many ways a direct sequel to the original, even bringing back one of its stars and introducing a monster with its origin in the events of the original.
4. Godzilla and Mothra: The Battle for Earth (H): Largely a pseudo-remake of the first two Mothra films, but pretty entertaining, though its environmental message could not be more heavyhanded.
5. Godzilla vs. Megaguirus (M): An interesting alternate continuity with some clever worldbuilding, an effective new monster, and the most badass heroine in the franchise.
6. Godzilla 2000: Millennium (M): Not bad, with good production values, but disappointingly routine and nondescript for what was supposed to be a brand-new universe and the debut of the Millennium series. It's also the only Japanese Godzilla screen continuity where it's unclear whether the 1954 film is even part of its backstory.
7. Godzilla vs. Biollante (H): An ambitious but highly flawed film with too many plot threads that don't come together -- including a title monster that is essentially extraneous to the plot of the film -- but with some really good ideas and moments here and there, like an attempt to examine how Godzilla's existence would affect the world and to explore some ethical questions about scientific responsibility that echo the original film.
8. Godzilla against Mechagodzilla (M): A mediocre attempt to revive elements of the original Showa continuity, with a very pretty leading lady but cheap-looking production values and a weak climax designed to leave room for a sequel.
9. Godzilla: Tokyo SOS (M): The aforementioned sequel, as well as another Mothra semi-remake; about on a par with the previous but with the cast inexplicably replaced.
10. Godzilla: Final Wars (M): A noisy, cluttered mess -- not so much a Godzilla movie as "The Power Rangers enter the Matrix on Independence Day, guest-starring Godzilla." Aggressively stupid and hyperactive, but some of it is ridiculous fun, such as the over-the-top scenery-chewing villain and the deadpan tough-guy American captain who sounds like Scruffy from Futurama.
11. Godzilla vs. King Ghidorah (H): A revised origin story for Godzilla, but it features an incoherent time-travel plot, as well as being a disturbingly jingoistic movie that glorifies the WWII Imperial Japanese military, putting it at odds with the politics of other films in the franchise, especially GMK. Also, the WWII-veteran characters barely seem any older in the 1990s portions than in the 1945 portions.
12. Godzilla vs. SpaceGodzilla (H): The dumbest Godzilla film since the '70s, with simplistic characterization, too many subplots that are unnecessary or fizzle out unresolved, and middling-to-horrible effects. Coming after the superlative Mechagodzilla II makes it an even more profound disappointment. Its one virtue is that it's barely referenced in the following (final) Heisei film and can be easily skipped without losing anything.
