<p>Can you suggest a tool for testing accessibility and section 508/ADA compliance of a Website with MS Share Point and .Net 2.0 as the underlying platform?</p>

In my experience, testing Sharepoint for accessibility is not worth it. Even if you've used the Accessibility Toolkit for Sharepoint (AKS) with Sharepoint 2007, the end result is far from accessible.
The trouble is that accessibility was not, and still is not a big consideration for MS when they made Sharepoint. Everything depends on table layout, and screenreaders are given a nightmare to deal with.
There are a few online tools - some will help validate your output, others pretend to test you for accessibility (
TAW
).
The problem is that many of the guidelines under WCAG are just too arbitrary, and will never be testable by an automated tool. This may change with WCAG 2.
Anyway, wish you the best trying to make Sharepoint accessible.
EDIT:
As a side not, I can highly recommend the following tools/resources for anyone interested in accessible development:
Chris Pederick's
Web Accessibility
Toolbar
NDA's Web Accessibility IT
Guidelines