After watching "The Pandorica Opens", my husband and I had to flip back to "Flesh and Stone" to see whether Pandorica Doctor matched jacket!Doctor, which he did. Red bow tie. But then we realized the Doctor's bow tie wasn't always red. So we looked at all the episodes in the series, and here's what we came up with:
1 - The Eleventh Hour - Red
2 - The Beast Below - Red
3 - Victory of the Daleks - Blue
4 - The Time of Angels - Red
5 - Flesh and Stone - Red
6 - Vampires of Venice - Blue
7 - Amy's Choice - Blue and Red
8 - The Hungry Earth - Red
9 - Cold Blood - Red
10 - Vincent and the Doctor - Blue
11 - The Lodger - Blue
12 - The Pandorica Opens - Red
Patterns, anyone? Largely, it looks like the Blue episodes tend to be the "monster of the week" ones and the Red episodes tend to be "conspiracy theory" ones - though 8&9 break that pattern. It also looks like the Blue episodes are in the past, though "The Lodger" breaks that pattern.
But most jaw-dropping was Amy's Choice, the only episode where the bow ties change color. The Leadworth!doctor has a blue bow tie. The TARDIS!doctor has a red bow tie. And the Dream Lord has a red bow tie, and so does the Waking!doctor.
And by the way, what does the TARDIS!doctor do at the end? Explode the TARDIS!
I don't know what it all means. But it's TOTALLY a clue.