Philosophical? That’s not how I recall it. 
Match Point is like Crimes and Misdemeanors without the annoying Woody Allen plotline. It’s quite tense though the main bulk of the film, and then it evolves into an extremely black comedy–a satire, really, of Fatal Attraction-esque thrillers–with the existential bit in the end. I’d say it surpasses Crimes and Midemeanors, and indeed, may rank as one of the best films Allen has made. (Though I have to admit to not really being a fan of most of Allen’s stuff.)
The central theme of Rashomon questioned the fundamental existence of an objective point of view; each witness describes the scene not only from a different perspective, but attributing differnet emphasis and motivation to some of the actions described by all characters. It’s one of Kurosawa’s best and certainly most imitated films.
What about John Boorman’s Point Blank? Lee Marvin’s Walker wrecks vengence upon his betrayers (which includes the faceless “Organization” which can’t give him his $93,000 back because it’s become a monsterous bureaucracy of a crime organization.) The whole story may or may not be just a figment of Walker’s dying last moments.
While I can’t recommend it, cheesy as it is, Capra’s It’s A Wonderful Life should fall into the parallel universes category.
Stranger
Being John Malkovich, although I’m not sure how to classify it.
Oh! I just remembered: My second-favourite Orson Welles movie:
Mr. Arkadin
It’s a surreal and allegorical little picture, sometimes straight-forward philosophical as far as the dialogue is concerned, but more often cryptic about it.
For example, the protagonist (tasked with determining the identity of the mysterious Mr. Arkadin, by Mr. Arkadin) literally seeks for for “Sophie,” to find out what clues she might offer— another character (a pawn-broker,) when questioned, keeps offering him a “teleoscope” – which, although lensless, comes bundled with a free (binocular) case.
It is not one of Welles’ better technical achievements, but the writing is right up there with the best of the best.
Whoosh
The Wings of Honneamise (subtitled…)
Perfect Blue
Revolutionary Girl Utena (particularly the movie, especially if you haven’t seen the TV series it will be quite random)
Key: The Metal Idol
Gattaca
Tron
Destiny Turned on the Radio
Terminator 1, 2
Labyrinth
Toys
Metropolis (Anime)
Somewhere in Time
There’s the Jean-Pierre Jeunet trio:
Delicatessen
The City of Lost Children
Amélie
David Lynch’s collection:
Eraserhead
Twin Peaks
Mulholland Drive (already mentioned)
etc.
Mamori Oshii’s works:
Patlabor II
Urusei Yatsura: Beatiful Dreamer
Ghost in the Shell
Innocence
Avalon
Gosenzo-sama Banbanzai! (which IMDB doesn’t even have listed so I’m doubting there is an English release)
Possible Tim Burton films: (?)
Beetlejuice
Big Fish
Pee-wee’s Big Adventure
From Stanley Kubrick:
A Clockwork Orange
2001: A Space Odyssey (already mentioned)
Quite a few are just “maybes,” but so it goes.
Ah yes, the equally onomatopoeic sequel to Do Desu Ka Dan.
“Whoosh whoosh whoosh whoosh whoosh whoosh whoosh…”
I don’t think anyone mentioned Altered States, with William Hurt. One of my favorites.
Yet another vote for Waking Life for the Lucid Dreams category. It’s incredibly enjoyable for a film that provokes so much thought and discussion.
The Wizard Of Oz, with it’s switch from B&W reality to color fantasy, its dreams & symbolism themes, obviously qualifies.
Hm, now that Sage Rat broke the seal on anime, I’ll add Satoshi Kon’s Millenium Actress to the mixed/“is this a movie or real life” category.
Meaning of Life Python
You might like some of Luis Bunuel’s surrealist films. Check out “The Exterminating Angel” (frustratingly unavailable on DVD) and “The Discreet Charm of the Bourgeousie” in particular for flip sides of the same coin.
You might also like Roman Polanski, especially his “apartment trilogy” – “Repulsion,” “Rosemary’s Baby”, and “The Tenant.”