Jason Kottke:

"Ecommerce sites that are slow, time out a lot, throw bad errors, and are generally not very pleasant to use tend to have URLs containing "jsp", "servlet", or ".jhtml". Perhaps that’s an unfair generalization to make because sites using Java on the back-end can be implemented and designed properly, just like with any other programming language, but there seems to be a strong correlation nonetheless."

Absolutely. These sites fall in the "overly complex and expensive, what’s a user again?" category. Application servers are back-office systems, and if you directly expose their output to users you’re begging for trouble. Usage of extremely complex URLs and sessions for anonymous visitors are the most visible symptoms.
Anytime I hear a site was done on stuff such as Broadvision or other J2EE thingamagics, I’m thinking the decision process was probably done on pseudo tech-terms, such as Java is "The Standard" (only as much as ASP or PERL or PHP or half a dozen other tools that are standard because, well, lots of people use them). Then the project is launched regardless of cost-effectiveness (and is the project actually doable?), let alone usability.
By the way, hint to experts in newspeak, on the real meaning of "standard": "Widely recognized or employed [...] Commonly used or supplied". "Standard by decree" is an oxymoron unless people start embracing it (in acts, not words).
In fact I think these sites come from a parallel universe where the Internet has been inented in the USSR. Clunky, unnecessarily intricate, manpower-hungry, top-to-bottom tech that should work but, well not quite, and is used regardless of the people the system is supposedly made for. There must even be a hidden relationship of some sort between these two acronyms, J2EE and USSR.
I don’t have the expertise to judget the technology platform itself. But the catastrophic way it’s often used is plain to see. Is there a lack of high-traffic, successful and well done J2EE sites (that don’t require hundreds of techies to maintain and millions in Sun hardware to scale)?