I've always run my pages through w3.org's validation service, since I discovered that the current version of WordPress (2.3.3) creates errors that are NOT in my content. The most frustrating aspect of this version is that it kept totally screwing up my content (which WAS 100% valid), every time it was saved to the DB and then later recalled. Then I discovered that un-checking the box "Use the visual editor when writing" on the profile eliminated this problem.
Unfortunately, even though the editor no longer screws up my content as stored in the database (specifically, the embedded HTML), it still screwed it up when the content was displayed.
After a little investigation, I discovered the source of the problem. In the script "formatting.php", on line 71 within the function "wpautop()", there is a routine that attempts to make paragraphs that creates some real problems with otherwise perfect content. I have one page in particular (http://highseasdrifter.net/blog/?page_id=9) that creates 63 validation errors in w3.org's markup validation.
When I comment this line out, the page validates 100% (which it should, since my content is 100% correct). Although I no longer allow the WordPress editor to modify my content before storing it (un-checking the box "Use the visual editor when writing"), I suspect that this same function may have be causing the problems with these routines as well.
Granted, I've found the solution for my own installation... provided I remember to comment it out again, should I ever decide to upgrade again. Besides... I can't be the only one who has experienced this problem. Any chance someone might officially remove this line from the script?