I personally use the freezer method. I place a bowl of water in the freezer untill it starts to get small ice crystals in it then take it out, net fish, and drop them in. I figure it's as painless as could be, kinda like shooting ol yeller I guess. I have only had to put any fish down once and that was a small school of Neon Tetras with NTD. As soon as they hit the water they peacefully floated like a feather to the bottom of the bowl, no flashing, struggling, no gill movements, nothing, it was as if that water was the bright light at the end of the tunnel. I hated every second of it, but at least I saved them from suffering any longer.
My deformed guppy fry have all been Koi or cichlid food, although I don't have either anymore, but I am getting some puffers, so I guess there puffer food since I know they are healthy, just have defects and I don't have fry on a normal basis, so the fatty content won't be too bad.
The hammer method made me look like I just ate a lemon covered in choclate milk and BBQ sauce, just hearing it made me squirm. But then again, I used to use the "thump" method on rats and mice for my snake, CO2 is SO much easier on me (I love rats) and the rats, and MUCH less messy.