I've purchased a number of games (mostly through Humble Bundles) that have both a Linux version on Steam and a standalone Linux version.

Would there be any performance benefit to running the games as standalone versions instead of through Steam, or are there no differences?

I'm trying to decide how I want to install my games. If the game is the same with or without Steam, I will go with the Steam version, so all my games are in the same place and receive updates automatically. If there are performance or other benefits to the standalone versions, then I'll go with that.