Wow... there are 12 I can think of. Pretty awkward, but here goes...
Beach Boys - Don't Talk
Dinosaur Jr. - Not The Same
Final Fantasy VII - On That Day, 5 Years Ago
Final Fantasy VII - Interrupted by Fireworks
My Bloody Valentine - Sometimes
My Bloody Valentine - Moon Song
Radiohead - Motion Picture Soundtrack
Serial Experiments Lain - Hitoribatchi 1
Smashing Pumpkins - Galapagos
X Japan - Forever Love [even though I can't understand it]
X Japan - Art Of Life
X Japan - The Last Song [see 'Forever Love']