Theoretical information:

1) You can put the weight (or lack thereof) where YOU want it (stronger rims/lighter hubs visa versa...)

2) As a lighter person you can have a very light, strong enough for you set of wheels for (theoretically) less $$$ than a similarly light set would cost from say Mavic (whose building wheels for 165lb men)

3) Customized BLING (King or Hope hubs....drool....of course King hubs will set you back to costing what a prebuilt set is gonna cost)

4) As a lighter person you can get rid of the bladed spokes and deep rims that are popular now (but which blow us small, light folk all over the road!!!)

5) Allows you to spend the money where you want it: Really care about the hubs sacrifice the rims...really want carbon aero rims sacrifice the hubs.

bla bla bla, drivel drivel, etc, etc. Basically it boils down to getting a set of wheels built for YOU which I imagine is very nice. Based on my basic pricing comparison it is true that you can indeed get a much nicer (read lighter but still durable and nice) set of handbuilt wheels with tried and tested components (Mavic Open pro rims, something like Ultegra hubs) than you can prebuilts in the $500-650ish range. When you are talking $1k wheels I'm not sure if the distinction is there (this is especially true if you can build them yourself or if your shop gives you a deal on labor).

I'm waiting on my new bike to be built up. It came with a pair of custom hand made wheels (King hubs, thin spokes, and some sort of nice low profile rim). I'll let you know what I think about them compared to my Mavic Ksyrium Equipes when I get a chance to ride them (but bear in mind I'll be comparing a pair of $1k custom wheels to $450-500 stock wheels; most of that $$ being in the King hubs...)