The Geth, Krogan (if you consider the uplifting) and possibly the Reapers from ME. Collectors as well if you count the genetic alteration of the Protheans.
If you follow the book canon for Star Trek, then the Borg were made by the Caeliar(and humanity, accidentally), so them too.
Uh, there's also the Sentinels from Halo (though they're not inherently bad). And any number of artificial constructs from World of ********, left by the super Dwarves or whatever the frak they're called.