PubCat is a utility to combine two Publisher files. It is able to rotate pages to insert landscape publications into portrait ones (or vice-versa) and can deal with linked text boxes. It requires .NET Framework 2.0, and runs from the command-line. Fuller documentation can be found in the readme.txt file inside the archive.
Currently PubCat will only run if you have Publisher 2007 and its PIAs installed (i.e. Publisher 2007 installed after the .NET framework). I'm working on getting it to work with Publisher 2003, too.
Download PubCat here