I spend about $900 a year at Newegg to build/upgrade 3 PC's at home, plus building for a relative. Never had any problems with them. In the past 3 years I've gotten:
1 barebones system with Nvidia 405 chipset board
3 Antec power supplies
5 motherboards (690G, 690V, 2 ASUS 780G, Gigabyte 780G)
5 AMD CPU's (X2 3800+, two X2 4200+, X2 4600+, 8750)
3 Lacie brick external drives (love the Lego look)
3 external drive bays for legacy IDE
7 internal hard drives (2 WD, 1 Maxtor, 4 Seagate)
2 cases (Antec Nine Hundred, In-Win red race car)
3870x2
8400gs
two 3650
Soon to order a 4850 and a 4860 as upgrades for my wife and elementary school age kid. Me, I'll wait for ATI's DX11 cards, but I'll get it at Newegg.
If I hadn't had great experiences, I would not keep ordering from them.
I've occasionally bought things at Fry's (monitors, a couple of hard drives) but I'd rather just go there for movies, anime, DVD players, televisions and appliances. I really don't like Fry's graphics card prices, and their motherboard/CPU bundles, while inexpensive, often include less than stellar ECS boards whereas I've had better luck with a Gigabyte, ASUS and MSI in that order.