Two-way replication between SQL Server 2008 R2 and SQL Server 2008 R2 SP3 I know that in SQL Server you can't have two-way replication between different versions.

I wanted to know if SQL Server 2008 R2 and SQL Server 2008 R2 SP3 are considered "different versions"?

Did anyone try to build a replication between those 2 versions?
Those aren't different versions just different service packs. Replicating between 2008 and 2008 R2 would better fit that definition of replication between two specific versions.

So The way I understand the MSDN article on the subject here is this 


  When you replicate between or among different versions of SQL Server,
  you are usually limited to the functionality of the earliest version
  used. For example, if you upgrade a Distributor to an instance of SQL
  Server 2008, but you have a Publisher that is running an instance of
  SQL Server 2005 and a Subscriber that is running an instance of SQL
  Server 2000, you are limited to the general functionality and
  replication functionality of SQL Server 2000.


And here is something more specific to merge replication


  For merge replication, a Subscriber to a merge publication can be any
  version no later than the Publisher version. For more information
  about compatibility for earlier versions, see "Compatibility Level for
  Merge Publications" 


In reality though, even if you can replicate between different versions, that can't be ideal. Replication is already complex enough by itself without adding in yet another layer of complexity. 

So if you can apply those service packs to the other servers, you should in my opinion.