Huh, is xpadder not free? Never heard about that.
But yeah, most games on steam have built-in controller support, while fangames usually don't, for games that don't have support directly you have to use something like joy2key or xpadder, both should work just fine. Most people I know use xpadder, but I use joy2key and it also works, and it's free (although it does occasionally pop-up a message asking if you wanna support the product)
Hope this helps, and good luck have fun with your fangaming