I have a windows 2003 r2 server with lot of users, websites , sql server , DNS , How can i move this to a fresh windows 2003 r2 including NTFS permissions without manually creating users , websites , db etc., its independent server, not in a domain.
Your big problem here is going to be the user accounts and NTFS permissions. To be able to move these across to the new server as they are, the only real way to do this is through backup as many have stated.
SQL is a bit easier, as you can backup all your DB's seperatly and restore them to the new server. However if your SQL db's use windows user accounts for permissions, your again going to have a problem.
With IIS, this can again be done by a restore of the metabase, or you could use a tool like IIS Export to move your IIS settings across, you'll still need to move your files though.
Your not going to find a way to do this with a single tool. With a mix of different tools then you will be able to get most of the way there, but I think your going to have an issue with user accounts and permissions without using backup.
Do not give up cloning idea: there is (should be) a way to substitute all the hardware-specific drivers with universal ones, then clone to new hardware, then install proper drivers.
Do you have AD? If not, convert your old server into DC, then connect new server as secondary DC. Be careful with SQL and IIS permissions: most likely they will be screwed after migration to domain.
Consider installation of whatever-is-used-for-authentication-in-non-AD-domains (LDAP?) on the third computer just to synchronize users of two computers.