Thanks.
I hadn't seen the post about themes controlled by
CSS, this certainly sounds like it would make things easier to work with from an accessibility point of view.
I must admit we'd not tried any pages with frames in as I have been adding content on our test site as html text, it seems they only occur when viewing an uploaded document? However as your link points out they are generally navigable with more recent screenreaders if correctly titled.
I'd like to give a bit of feedback from the point of view of using Moodle with a screenreader if I may, probably mostly stuff from W3C guidelines you've already considered for 2.0... sometimes validation doesn't pick up on contextual problems with accessibility, though. We haven't really had the opportunity to do a full audit, but hope this is of some use

The out of
context links and alt tags on text items seem to be our main stumbling points...
1. A number of links dont make sense out of context e.g. more
Users often quickly navigate a page by asking JAWS to read out a list of the links on it, this doesn't really work if it just says more
more
more
2. There are several images without alt tags or with alt tags which are confusing: this course allows guest users to enter which links to a particular course doesnt say what it is.
3. Use of tables for layout not ideal. Although JAWS seems to read through the layout in a logical manner (suspect other screenreaders may not do this as well though), it also reads out the table and column number before each piece of text, which rapidly becomes annoying.
4. In most of the content areas (e.g. when available courses is displayed on the
front page), what appear to be text links to courses, etc, have alt tags attached to them. JAWS only reads the alt tags which say resource or forum and you cant distinguish between them. The text itself is not read out.
5. There is a very lengthy menu on the left before you get to the main course content its very time consuming to go through this with a screen reader.
6. Problem with combi boxes, e.g. language box and menu which allows you select a course JAWS automatically selects the first option when you simply want to read the options, normally it will display the full list and let you move down the options. No idea why this is happening, though!