Strawberry Perl uses CPAN, which means that you are up to date as far as modules are concerned. When things are added to CPAN, you have immediate access to them. Strawberry Perl also comes with MinGW which means that Strawberry Perl can use quite a few XS modules directly from CPAN without any modification. The MinGW distribution comes with gcc, make, ld and other tools to help you build modules. I think Strawberry Perl also comes with a few modules that let you install PPMs (Perl Package Manager files).
ActivePerl installs modules using its own format called PPM (Perl Package Manager). The official repository is hosted by ActiveState. You can find PPMs for most of the popular modules so you shouldn't have any trouble unless you are looking for an obscure or really new package (so bleeding-edge stuff won't work because PPM usually lags behind CPAN). Although easier to install than CPAN modules, PPMs are specifically created for Windows and so some CPAN modules will not work (because they do Unix-specific things).
I have used both before and it seemed to work for most cases. But I lean towards Strawberry Perl because the environment is closer to Unix and so there are not many incompatibilities. On the other hand, ActivePerl is made for Windows and so it works with Windows very well.
Another option is to install Cygwin and Perl that comes with Cygwin. I have done that before and it works reasonably well. You also get access to CPAN.
Pick what you think works best for you.
