Royal Space Force: Wings of the Honnêamise
A film that captures the passion of the creators' love of flight better than anything else I've watched. The film is much more a human story handling issues of relating to others, discovering what is important to oneself, and what is potential of a vision. One of the most visually stunning animated works ever produced, and it still has that under-dog feel that early Gainax works had.
Patlabor Films 1 & 2
The first movie is more a standard, straight forward affair than the second film and I view it as more of an introduction to the world setting and the characters. The second film is an examination of Japanese attitudes and handling of political matters within the country and a potential path they could ultimately travel down. I highly recommend the second film, but both are worth watching.
Skycrawlers
A slower film than anything else I am listing. I did not like this movie upon my first viewing, but it wouldn't leave my mind when it ended. It took me two viewings to really appreciate the tone and pace that it had, and it deals with some pretty heavy topics including the effects of war on individuals, obsessions, repeating mistakes, and much more. More of a light science-fiction, but check it out.
They Were Eleven
This is framed as more of a thriller- ten students attempting to get into a prestigious university must live together on a ship for an entire orbit around a planet unsupervised to be considered for acceptance, but there is a mysterious extra person aboard. Who is the odd one out? A really great cast of characters that focuses on racial tensions, identity, and trust/mistrust.
Cyber City
This is a three episode OVA with a different character taking lead role in each one. The first one is a very simple action hero type of film. However, the second and third are character and philosophically driven. They aren't the greatest stories ever told, but there are some really interesting concepts and ideas wrapped in a later 80s/early 90s presentation.
Macross Plus
A really wonderful four episode OVA that (like Royal Space Force) showcases the creators' love and passion for flight. It is much more about the relationship issues between the three primary characters and their struggle to find/retain their purposes in the world. The visuals and music are worth watching this for on their own, but the story is complimented by them, not overshadowed.