My last few SoC based designs have booted from SPI NOR chips - although that may just be the way TI are going at the moment. It does make for easier provisioning at manufacture, though, and prototyping is no harder.
(And Freescale reference designs - fine, until you get off the beaten track. I'm just doing a Coldfire MCF54415 design - reference designs are few and far between. There's an unavailable elevator card for it, but other than that, not much. Odd!)
Edit: But yes, ripping reference designs is a good start if at all possible. Software people tend to be happier the more a design looks like a reference board, too, if at all possible, especialy if they've been developing on the reference board before the real hardware turns up. Keep a changelog of IOs you've moved, added or deleted, to make life easier for all.