I like the thought of future proofing, but I think that with the rate of change in hardware characteristics you just cant account for (new sockets, moving from agp to pcie, ddr2 to ddr3, etc) it's certainly difficult to do effectively beyond more than one or two generations. My last system from a few years ago, AMD s754, I ended up just parting out before I cba with attempting to modernize it.
However, with that in mind this time around I tried to 'future proof' other components instead. A case I can keep for years to come (god forbid something replaces atx, lol), fans that will perform and last well, a powerful, quality modular PSU (Most changes to PSU tech can be accounted for with some simple adapters, at least as far as I recall), and good hard drives and disc drive.
Trying to future proof your GPU/CPU/RAM/Mobo is just tough. I did go with an AM3 board in hopes of going Bulldozer in the future; but on that same note I'll be kind of surprised if I consider a CPU upgrade worthwhile before they decide to push a new socket. And by that time, if you need a new motherboard you'll probably also be looking at new ram and a new HSF and a new CPU at the very least.