WSSv2 does not support ASP.Net 2.0 web  parts - you need to create your web part
in VS2003 using ASP.Net 1.1 and the SharePoint web part  interfaces, or deploy
your ASP.Net 2.0 web part to the WSSv3 beta instead.

But when iam surfing net regarding this issue.

I found one article which says WSS with SP2 is enough to execute the
VS2005 webparts only thing is we need to configure the website to
V2.0. I tried in that manner but no use.

Did anyone tried this?

The article is incorrect, or you misunderstood. WSS with SP2 will allow you to
run ASP.Net 2.0 on the web  server, but does not give you the ability to use
ASP.Net 2.0 Web Parts. The only way to run an ASP.Net 2.0 web part  on WSSv2 is
to use a wrapper like Son of Smart Part.

Just now I gone through this article

office.microsoft.com/.../HA100806971033.aspx#4

Can anyone help  me out how can I deploy  or run my Webpart which I
developed in v2.0?

I mean is it like normal stsadm or do u need to take any other way?

If you read the "Implications for Web part  development and deployment" section
of the article you linked to, the answer is there:

Can I use ASP.NET 2.0 web  Parts on Windows SharePoint Services with SP2?
Not as Web Parts. Given that all Web Parts can be treated as standard Web Form
controls, ASP.NET 2.0 Web Parts can be added to pages running in Windows
SharePoint Services with SP2, just not within Web Part zones. In this manner,
such Web Parts will behave no differently than standard Web Form controls, and
should have been written with this contingency in mind. Out of the box, Windows
SharePoint Services will not use any ASP.NET 2.0 constructs. At the core level,
SP2 will not change the rendering behavior of Windows SharePoint Services. In
other words, Windows SharePoint Services will not suddenly gain the ability to
use master pages or ASP.NET 2.0 Web Parts. Until the next major release, your
only course of action is to take an approach of encapsulating an ASP.NET 2.0 Web
Part with a Windows SharePoint Services Web Part designed for this purpose. You
might want to investigate http://www.smartpart.info for an example of this
technique.

I am able to deploy  .NET2.0 webpart in WSS with sp2.

For this first I changed the virtual folder to run under .NET2.0

blogs.tamtam.nl/mart/SharePointOnASPNet20.aspx

After this followed the article

office.microsoft.com/.../HA100806971033.aspx#4

This is link which helped me a lot

blog.spsclerics.com/archive/2005/12/09/30651.aspx