Bob Dylan once said "their chords were outrageous...just outrageous" while describing the Beatles' music.
Just in case the word "outrageous" does not impress the serious musicologist in you, here's a fantastic scholarly analysis of the the band's work. (If the site is down, read it from the cache.) Via Digg.
A question that often pops up when reading such papers is "did the Beatles themselves understand the musical underpinnings of their songs like these scholars do?" The implicit assumption there being pop music is all about "feel" and "instinct" and pop songs are not written or composed like classical music. I find that hard to accept. Demo tracks on "Anthology" ("I'll be back" is a great example) are proof that only rarely did the songs "arrive" fully realized. Besides, a musician, like any creative artist, has to make good choices. So whether or not John and Paul understood the technical implications of using incidental chords or starting a song in one key and the verse in another, they certainly had to know what choices made for a great pop song.
Soundscapes has an entire section titled "Beatles' Studies", with papers like "A flood of flat-sevenths" :)
For a "music-only" analysis of the Fab Four, nothing comes close to the great Alan W. Pollack's "Notes On" series.