I've confirmed this issue. It does take a very long time to create an exe from the basic script you posted. Checking the list of dependencies, and therefore packaged modules I notice Any::Moose which then requires Moose or Mouse depending on your setup. I have no experience of using either, however I've been told by others that Moose (at least) is pretty bloated. This may not be true, but either way there's a large dependency list from the simple script below.
For clarification my setup is Windows XP SP3 (I know, it's a wortk thing), Strawberry Perl 5.12.3, PAR::Packer 1.013. Older Core 2 Duo laptop, 1GB RAM.
The script I used:
The pp command pp -v -o mongodb.exe -x mongodb.pl (cut down from vvv and vv in an attempt to generate output less than 233KB). mongodb.exe is eventually created, and produces the output expected. There's nothing obvious to me in the logs (vvv, vv, v) as to what the hold up was. Perhaps someone else has packaged MongoDB and has more experience to draw from.