Dude... I just feel sorry for you and your friend

I was in a situation similar to yours, but I was recommending a computer. He was looking at some weird Alienware systems, and I just shook my head and pointed him at a Dell deal from FW. He saved $1000 right there. I told him he could build one as good as the $2600 Alienware system he was looking at for $1100 parts, and he said he didn't want to deal with the time. That's one argument non-computer building people have.
And I help random people out in my building. De-virusing AOL webcam-ed people, printers not working, even reinstalling XP from scratch on infested computers. And I don't charge a cent, and out of goodwill.
Sometimes people don't even know what they have!!! Example? A girl downstairs has an IBM laptop, and got a PCMIA ethernet card. When trying to fix her USB printer, I was checking cables and asked why she had an extra card. She said the computer didn't have a ethernet jack. I take a pencil, pop off a plastic cover over the ethernet port, show her, and she didn't even know it was there!!! People can be taken for a RIDE....
I'd just tell him that he had a not so good deal. Be honest. He can take issue up with the people that built it if he wants, and maybe they will give him a refund once he finds out what they did. Explain things to him clearly and professionally, and don't say 'you got screwed'. Just tell him they charged him 60% more than the parts cost, and show him a comperable deal at Dell or somewhere [normal, no coupons/rebates/FW stuff]. I don't like leaving people uninformed... knowledge is power, ignorance is weakness.
Full disclosure: A computer I built from scratch for $350 has a 1800+ at 2.2ghz, 512Pc2700, 120GB 8mb cache, and various ameneties [Antec case/ps etc], and a Radeon 9100. And it gets ~7500(±10%) on 3dMark2k1SE.