What changes should be made in an application while migrating from ie8 to ie9 regarding css,html, javascript,DOM
Compliance with W3C standards. That's all.
Internet Explorer 9 is Microsoft's way to full Web Standards' support.
In most of the cases, you'd remove previous versions' CSS, DOM hacks. Or conditionally allow them for versions lower than 9.0, in order to render your pages in standards mode.
Now you can take advantage of some CSS 3.0 and HTML5 features, but keep in mind that most of them are working draft, yet to be approved by W3C and browser support in other navigators can differ their expected behavior.
Check this MSDN index if you want to learn more: