Here's what I'm running with right now:
Guitar -> (Fuzz Face) -> JHS Buffer -> MXR Compressor -> VOX Wah -> EHX POG 2 -> Bluesbreaker -> Morning Glory -> Signa Drive -> Tap-a-whirl -> Boss CE-2 Chorus -> Volume pedal -> Boss DD-7 (with tap tempo) -> DL4 (with expression knob) -> BBE Sonic Stomp -> Boss Tuner -> Boss RV-5 -> amp
I did what we all do and got sick of what was already kind of working, in favor of something that might work better. It looks really different because I moved a lot of stuff around, but the only actual new pedals are the Cusack Tap-A-Whirl, which I'm still getting used to, and the JHS Morning Glory, which is awesome. And also the Fuzzface, though that's not a normal part of the board, since I don't normally need fuzz, but it's really easy to plug in if I need it. I also cleaned up some of the mundane stuff. I moved the buffer underneath the pedalboard, like so:
So that all I need to do is plug in to the bottom of the board, and it looks pretty slick. I got a second Pedal Power 2+ and mounted it underneath, so now every pedal has it's own channel on a power supply. And because I now need to run two power cables, plus an amp send line, from the board, I home-made a pedal snake by getting two long power cables and zip-tying it all together. I think I need to get some kind of covering for it, though, since you can't run it through your hands. I'll look into that.
The only thing that I know will absolutely change in a bit is I've finally caught up with 2008 and ordered a Timmy. So that's going to go in the place of the Bluesbreaker pedal, which is great but isn't as versatile as the Morning Glory, which based itself upon the Bluesbreaker anyway. But for now, I'm using the Bluesbreaker as I would the Timmy; as a cleanish boost and to push the other overdrives. I love the expression knob on the DL4, since it lets me control whatever I want, which right now is just repeats on all of my delays. And so far the layout is working out pretty well, since it's protecting the pedals I want to protect (compressor, sonic stomp) from my foot while giving me good access to the rest of them.
As far as amps go, I'm digging my Valve Jr. for plugging straight in, but with the pedalboard I'm finding I like the ability to tweak some of the brightness out, so my Blues Jr. lets me do that. I've really only been working things out with my new Strat, though, so we'll see what happens when I try out my other guitars. But for a good Strat, this setup is pretty killer.