SQL Server 2005/2008 are both free.
Express may or may not be "the same as SQL Server 2005/2008" depending on the use required. For the most part, it is equivalent in that it has all the same data types, etc.; however, the Express versions do not have SSIS availalbe (and a few other "minor" features ;-). So, if the software vendor is specifying, for instance, "SQL Server 2005 or 2008 with the latest service packs" or "SQL Server 2008R2", then, no, it would not be equivalent.
My os is Server 2003
This sounds like you are planning on deploying the software and, more significantly, SQL Server as a network application. If so, then you need to spend the money to get a non-Express and non-Developer version of SQL Server because neither of those are to be used deployed on a network.
Che3ck out the following conncetions to compare the versions:
http://www.microsoft.com/sqlserver/2005/en/us/compare-features.aspx
http://www.microsoft.com/sqlserver/2008/en/us/editions.aspx
