The Agile enchantment seems to be one of the more obscure weapon enhancements in Pathfinder so I'm not surprised that it doesn't seem to be included in PCGen. Even so, I'm requesting that Agile be included at your earliest convenience. A Dex to damage enchantment would be really nice to have in PCGen. To say nothing of the fact that it's PFS legal, so I'd love to have an Agile enchantment for any CQC weapons without having to get the Weapon Focus and Slashing Grace feats.
For reference, the Agile enchantment can be found on Page 21 of Pathfinder Adventure Path #100: A Song of Silver.