Hi,
first, I would like to congatulate you on really outstanding job - in my opinion, this utility is true diamond :) And I know a bit about it, as my organization maintain it's own utility of this kind for internal testing purposes.
Here are two things I would like to be able to do and I can't (or maybe I just don't know how to do it), first is critical IMHO, second would be nice:
1. crawler - possibility to crawl only part of site, only URL either including or excluding (regex?) particular set of patterns. It's very important, when you need to repeatedly fix/re-test only small part (some pages) of large site. Also easier to separate and browse raports
2. crawler or report - possibility to exclude from analysis (parsing) parts of page, for example framed in pair of special HTML comments (like <!-- no parse-->). For example comments section can be left out due to large amount of external link in it etc.
3. Ability to Authorize crawler would be nice, as often in final developing stage site is already on production server, but anonymous access is disabled
these would make me happy :) Also small bugs? (not sure if its intended behaviour):
1. missing resource (for example image) on site with custom 404 redirection reports all kind of content violations, but in fact these are custom 404 page problems.
2. default content-type of *.js files served by IIS is "application/x-javascript", SEO tolkit flags it as incorrect (suggesting "application/javascript" instead).
And last question - how to perform logical OR in query (for example URL contains XXX OR YYY)?
Cheers