Sean: It would of course be possible to have the incoming email handler put the contents directly into the database. Perhaps that's a better way of implementing it. I just thought that using HTTP POST or XML-RPC would involve slightly fewer dependencies for the script. A pure Perl implementation is easier to install than having to compile/link database libraries. For example Oracle client libraries are a bit hairy to link against.
Regarding the dot-qmail files, that should be up to the user/administrator and would depend on the application. On some sites you would obviously want more granular control of what email goes where. If you were implementing OpenACS Webmail (there was actually a webmail package for ACS Classic once) you would use a .qmail-default file. But using .qmail-default does not preclude the possibility of having other .qmail files; .qmail-blah-default would IIRC override .qmail-default.
I agree that qmail is a breeze to install and administer. But let's not turn this into a mail server flamewar 😉. Both of the approaches I've outlined work equally well with all mail servers (I think; if that turns out not to be the case, then start the flamewar).
