Line merging is possible to achieve using Adobe Acrobat 8 and AutoCAD 2008. I just confirmed it and here is the result with lines merge and lines overwrite.

The built in DWG to PDF.pc3 that comes with AutoCAD cannot do this and if you just use the Plot command and the Adobe PDF.pc3 it will not work.
In short here is how.
- In the Page Setup select Adobe PDF.pc3 or some other pc3 file that supports lines merge. Click on Properties>Devices and Document Settings>Graphics>Merge Control and there you select Lines Merge.
- Acrobat PDF Maker must then be used. Either via the toolbar or with the PDF command.
In step 14 in the post below you don't have to retain the layers. Flatten all layers works as well.




