This leaves you the ability to not have to create an ODBC connection on each target machine and point the program to a new server on the fly.

I have written an application that takes in a fixed-width file (thanks in no small part to advice I recieved in a seperate thread) and then dissasembles each line, runs a fairly meaty SQL SELECT ...

SQL Server 2005's Type 4 JDBC driver provides database connectivity from a Java application. Though the driver class and connection URL are a bit different in this version, connectivity is a snap.