I tried GitHub for Windows but found it a bit dumbed down. Switched over to Atlasian's Source Tree and never looked back.
I had some problems with it keeping changes synced with the file system, though (on Mac OS). E.g., I'd change something in my editor and SourceTree wouldn't pick it up until I reopened the repository in SourceTree.
I also prefer a single window like GitHub's app, but that is a minor annoyance. The non-syncing made SourceTree unusable after a while, and I went back to GitHub for Mac.
I wish Atlassian would put out an update, because I'd prefer to switch back.
I'll try GH Desktop, but for the past few months mine's been broken where it loses my repos, so I've been using ST exclusively :)
(I don't see why this is being modded down - is it because I failed to mention I'm also using it in Windows?)
[1] http://gitup.co/