we are using Domino 8.0.1 on windows server 2003.now we want to upgrade to 9.0.1 on WS 2012.
please tell me the things to keep in mind, detailed steps to to follow to migrate already running web application on upgraded version.
Thanks.
Subject: My experience
I never had any issues upgrading between versions. Especially from 8.x to 9.x I don’t see any issues.
My suggestion is to first update the servers, then the clients and finally the mail templates.
Web applications (just like all other applications) should jsut work, it is after all IBM and Notes we are talking about, not some Microsoft product where every version upgrade becomes a full-blown migration. 
The only issues I seen in the past is when going from 5.x to 6.x and I had agents with my own Join(), Split() and Replace() functions. Those functions were added in Notes 6.0 and broke my code. But ever since, there have really not been any cahnges made to the Lotusscript language. There are new properties for classes as well as several new classes, but as long as you (or your developers) wrote code properly, you should be good. When I say “properly” I mean using GetItemValue() and ReplaceItemValue() instead of using extended notation (e.g. doc.MyField=“foo”).
Subject: Upgrading to Domino 9.0.1
Here is a comprehensive documen for upgrading your srver:
Upgrade Central: Planning your upgrade to IBM Notes and Domino 9.0.x