Finally, i compeleted my WAI related things and here to share my experiences.
The tools that really helped me are again W3C validator(BTW W3C itself rollsout the spec) and ATRC Accessibility Checker which is developed by Adaptive Technology Resource Centre based upon the proposed Open Accessibility Checks (OAC).
I used W3CValidator to check WAI and XHTML markup validation.It is a great tool and you can provide either the url to validate or directly upload the content through file or inpput textarea.The result of validation shows level of violation(Error,warning,etc) with the line number of the content provided.
Here's an example,
Accessibility Checker tool was setup on a machine ,it gave results in a browsable manner dividing pages int ot tables,frames,images,etc.It also shows the part with violation in results.The installation is trivial.It requires JAVA and Apache Tomcat for working.
Bobby(from WatchFire) is a windows desktop tool which spiders the particular web application and runs checks on all html pages.But as we were not working on pure HTML it was not useful for us.Reports are again browsable with abilty to make projects ,have scheduled checks, nad many more features.