Lots of great stuff already mentioned - notably Baraka and Koyaanisqatsi. Let us not forget also:
Powaqqatsi: Life in transformation (1988 )
Naqoyqatsi: Life as war (2002)
I tend to mute the "Qatsi trilogy" aforementioned and put different music on however - even in groups, we have experienced some amazing synchronicities while watching.
My personal favs:
Mulholland Drive - Exceptional piece of mind bending, immaculate film making.
2001: A Space Odyessy
Primer - Best time travel film. Ever.
Milo and Otis - such a nostalgic film for me.
Gummo - Haunting film by Larry Clark
The Machinist
Pink Floyd, The Wall
Children of Men - Really is one of my favourite films of all time
Earthlings - Must see documentary on animal exploitation and the meat industry.
There are loads more!
I am a piece of knowledge-retaining computer code imitating an imaginary organic being.