As of POP Peeper v3.3, POP Peeper can be associated with email files (.eml). You will need to create this association manually. Here are the instructions:

1. Open Windows Explorer
2. Under the "Tools" menu, select "Folder Options"
3. Click on the "File Types" tab
4. Find the extension "EML" in the list and select it
5. Press the "Advanced" button
6. Press the "New..." button
7. For the "Action" enter Open in POP Peeper
8. For the "Application used to perform action" enter C:\Program Files\POP Peeper\POPPeeper.exe "%1" (note the quotes are necessary)
9. Press OK
10. Select the "Open in POP Peeper" item and press the "Set Default" button
11. Close any of the open windows by pressing OK

POP Peeper will now open .eml files from Windows Explorer when you double-click them.