Well JP, I'd say he took you to the cleaners!
J/K of course...
To me the knowledge involved in setting up the system/components/OS/software/etc is worth it's weight in gold to a customer. Sure everyone can order parts cheap online, but not as many people as you might think can piece all of the parts together. He didn't have to research any parts for compatibility, spend any time reading through instructions, or have to fumble through software installs (fdisk--what's fdisk?!

).
He got a nice system with major perks--new leather manager's chair & personal workstation--even I'm jealous now, I've seen those chairs and that desk sure sounds a bit better than my $45 WalMart special!
So of course he's satisfied.
You put around $500 into a project and got around $275 profit from it. As Thud mentioned you made anywhere from $18-$27/hour (sweet!) and I'm sure you didn't exactly
hate doing it right? I would love to be able to earn 150%+ profit on a computer project that I actually enjoyed doing.
I look at it this way...I have around 40 or so people in my work center and at least half of them have asked me for computer tech support at one time or another. The MOST valuable thing that I'm losing is my time...can't put a price on that.
So did you charge him to much? No
Did you earn your money? Yes
Did he get a fair deal? Why certainly
Are you both happy? Let's count the smiles:

Yep!
You should feel quite good about that transaction...
My $.02
Mike