Been thinking about this a lot today, but I've been finding it very tough to pick, especially as I don't like to put multiple films from the same director into lists like these. So many of the films I like the most also have something in them that bothers me, or otherwise need some kind of qualification to appreciate - I would struggle to write Golgo 13: The Professional in good faith here, for example. Added to this, there are more than a few embarrassing gaps in my viewing that might have helped me out, but we'll not dwell.
On the whole though, I'd go with
Aim for the Ace!
Maybe a bit left field, but I think this is a really solid sports drama which shows the Dezaki/Sugino tag team coming into their own as a force for visual storytelling. Just because you're a film about a teenage girl playing tennis, doesn't mean you can't also rock the neo-noir look.
The Castle of Cagliostro
Honestly, I was torn between this and Porco Rosso, as I wanted to limit my Miyazaki quota. Of the two, I think this is more accessible though. It's a beautifully told adventure with something for everyone; you don't need to know anything about Lupin, Japan or anime in general to get it - it just works. There are those who maintain it's somehow disingenuous for not staying true to the Lupin of the manga, but frankly, they can fight me. Lupin anime has been borrowing from this film for more than thirty years; it's canon, deal with it.
Millennium Actress
You can't not have Satoshi Kon, but what if you could only have one? Perfect Blue probably is his best film, but it's not something I could put on anytime. I'm very nearly in agreement with Neil about Paprika, but I have a couple of small reservations. Tokyo Godfathers is delightful, but I think it's Millennium Actress that has the most potential to reward you and reveal new facets of itself to you every time you watch it.
Ghost in the Shell
Do I even really need to write something here? I'm in the small and unpopular minority who like Oshii's first Patlabor film more than the second and I'm not sure I can really justify that. GitS though, while it frustrated me as a kid, I think has increasingly won me over as time has gone on. I can bathe in this film; its sense of mood and place and atmosphere are so tangible. I suppose it's Oshii at his most him, stripping out humour and outer personality to leave us with an intensely inward looking film, but isn't that the point?
Macross: Do You Remember Love?
While it compresses and removes a lot of characterisation from the series, I think this breezily old-fashioned tale of space-borne derring-do does a truly remarkable job of elevating a tv serial beyond the typical level of the obligatory compilation movie, and forming it into a real big screen spectacle. In an era that brought us many great looking films, this still stands up there with the best of them, a gorgeous swashbuckling yarn, flinging missiles and singing kitsch idol songs to save the universe, and somehow making us believe that could work.