For me, it has so much to do with the personal connection I have with said album. Where did I buy it, what was going on in my life.
In the case of Miles Davis, my favorite is still the classic "Milestones." While there's little to dislike about this great record, this is a hard sale to the world at large due to Miles' prolific output and "Milestones" proximity to one of jazz's most beloved albums, "Kind of Blue."
I was given "Milestones" as a record when I was a teen and it was one of the only albums available to me at the time. Along with Dizzy Gillespie's "Sonny Side Up" and some great Beatles albums, "Milestones" was on heavy rotation. This is still some of my favorite Cannonball on record as well. It is also, in many ways, a transition album from Miles' records that sounded like live sets of music ("Milestones" has a piano trio cut on it!) and albums that have Studio Purpose.
I got on this topic last week after a nice dinner in Portland with some old friends. We were talking about Radiohead, and I asserted that my favorite album is "OK Computer." I got an amen from a stranger walking by, bolstering my opinion.
Agreements from strangers aside, however, "OK Computer" is primarily my favorite because of when I was listening to it. During my Master's in Jazz Studies at North Texas it provided the soundtrack alternative to all the brain-cramming I was doing during the days.
My musical knowledge tells me that "Amnesiac" with all it's awesome songs (I even covered "Knives Out") or "Kid A" with about the greatest opening to a record ever ("Everything in its' Right Place") should place as best, but the added emotions I feel when "OK Computer" comes on place it in a different category.
I guess in the end, as much as I try to learn about all the techniques that going into making great art, I still feel like it's the subjective nature of a work that seems to win out.