"Miskatonic U School Colors? Anyone happen to know what they might be?"
That's what launched this thread at Yog-Sothoth. The very helpful Gil Trevizo points out that Chaosium's "Miskatonic University" supplement specifies the schools colors as purple and black.
Me? As I wrote there, I vote for Cardinal Red and White based on the "WDBUD?" test. By default I assume that any attribute of Miskatonic University not specified by Lovecraft (or another author*) can be discovered by asking "What Does Brown University Do?" or some variation thereof. Brown claims Seal Brown, Cardinal Red, and White as their school colors. It seems fair to shamelessly steal two of those and leave the school it's namesake color out of respect.
Outside of that justification I have no basis for the red and white color choice other than the fact that I think it looks good.
* I probably should have written "another established author". If Campbell, Derleth, or Smith had said purple and black I'd give that color scheme some more weight.