I've used both, and both are fairly decent perl's.
It's easier, as a general rule, to build 3rd party modules for Cygwin, since it provides a fairly unix-y view of the system.
A few other things work better in Activestate, and AS also provides the ppm system, which lets you access binary versions of many modules.
For most uses, either one will do fine for you, I'd think.
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