I have to agree with this article by Randall Stross in the NYT about the limits of eBay. Although I'm an eBay buyer and seller and probably do about a transaction a month, I definitely agree that there are limits to the eBay model because of its dependence on caveat emptor. I've found that if you shop around, you can usually find what you are looking for without the hassle of going through the whole auction and checkout process. In many cases, it is much cheaper to boot.
Case in point, I recently purchased a Timex Bodylink watch/HRM/GPS from Bike-Run-Walk for much less than the final auction price (if you include the hidden cost of shipping, which is usually quite steep for eBay auctions).
If I'm looking for something unique or unusual, eBay is the place to go. But for most stuff I buy online, the more traditional commerce model seems to work better.