A PK3 is basically a compressed archive, like a ZIP file. So all you do is open up WinZIP, stick in all the files of your mod, (skins, QVMs, models, sounds, maps, etc.) save the archive, and then rename the archive from myMod.zip (or whatever you want the name of the pk3 to be) to myMod.pk3, and voila: you have a pk3.
Weapons Modeller for Siege 2
, a Half-Life 2 Fantasy mod