When you produce Boons, for example in the Godswood, you'll be given the option to add a bonus. Click the bonus button, then click a Blue Gem to apply it to the boon.
See the Blue Gem page - though we are waiting for a template to be added to it momentarily by Razorgirl, our admin.
Whether they're safe to use or not has not yet been officially confirmed on the Wiki itself (developers rarely test things in the game these days, they use a sandbox server which can produce different testing results in the game). I'll test this on a few types of boons, anyone else who can test will be good help too. :)
I've produced boons within the Godswood. More speciffically, 10 common boons. I added blue gems, and 7 of them turned out rare. For now, I can say it works. Anyway, I can't confirm with only 10 experiments. When I've finalized at least 50 boons with blue gems, I'll let you know if it's working or not.
I've tested on just 5 common boons so far (I had to sleep! :P) and they all turned out normal and common. I'll keep checking too.
It's possible it might be a platform-related thing? Which platform are you guys on? I primarily play GoTA on Kongregate, though with Facebook connected to Kongregate I can play it on Facebook too if I could be bothered to log in (Facebook has kinda lost its charm).
I've recorded a series of very peculiar results, but this is the end result. The first 10 times proved to be only lucky shots, or maybe a bug, not that I complain about it ;). After producing another 26 various boons from the Godswood with added blue gems, I can give you the end result: enhancing boon production with blue gems results in producing more of the same boon at once!!! E.g. for my biggest success so far, I obtained 4 Legerdemain at the end of only one cycle of production. THIS IS IT. THIS IS HOW BLUE GEMS WORK FOR BOONS PRODUCED IN THE GODSWOOD.