At the moment, I basically keep good track of what CPAN modules I use and keep them in a app-specific perllib and also say in the dev notes that this is so, and it'd be a good idea to install these modules yourself (a Bundle is used, at the moment)

Actually, Bundles are (and have always been) kind of a dirty hack. The newer trend is toward Task modules, which themselves are implemented using Module::Install. See the docs in Task for a more detailed explaination.

I know of the Best module, but the low version number and long-time-since-hacked-upon date makes me wonder how good it'd work as well.

I have used Best and it is totally stable and production worthy (IMO of course).

Low version numbers don't mean a thing, nor does it matter how long ago something has been hacked on (unless you are talking like +5-6 years, in which case the module may not be in keeping with current community best practices (no, not the Damian's book, the communities best practices, there is a subtle difference). In the case of Best the code is so simple that I would be more worried if there more releases. If you look over the Changes file you will see that most of the releases have been for doc fixes and a few minor bugs which tells me that other people are using this module and that the author cares about clarity of his documentation, both very good signs.

I hope people can understand the importance of having a fall back, pure perl implementation of some of these modules. I do understand that in many instances, these modules are much much slower, but it is better than nothin'.

I disagree with the importance of Pure Perl fallbacks, they are nice to have in some cases, but really, just about every *nix system comes with a C compiler and with the existence of things like Strawberry Perl the Windows platform is becoming less of an issue. IMO, effort is better spent making it easier to compile and install C based extensions then it is spent re-writing these extension in a slower Pure Perl version.

Is there a better method that you guys use?

If you are looking to distribute your code easily without your users needing to install 1/2 of CPAN, then you might want to look into PAR, which is about as close to PHP-ease-of-installation as Perl gets these days.