I recently needed to merge two PDF files containing the odd and even pages of a document. You can do so using Adobe Acrobat (I got a free trial here).

You need a small script for this, I found it at PlanetPDF and put together a sequence for Acrobat's Action Wizard.

1. Download the file:

2. Then go to File > Action Wizard > Edit Actions > Import, select the downloaded file.

3. Close the "Edit Actions" Dialog

4. Select File > Action Wizard > Merge odd and even pages

5. Click Next

6. Click Add Files > Add Files and select only the file containing the odd pages.

7. Click Next, click "proceed to Next Step", click "OK"

8. Select the file containing the even pages.

9. Choose where to save the combined file

10. Done!