When comparing GitEye vs GitHub Desktop, the Slant community recommends GitHub Desktop for most people. In the question“What are the best Git clients for Windows?” GitHub Desktop is ranked 17th while GitEye is ranked 22nd. The most important reason people chose GitHub Desktop is:
This is the official GitHub desktop client built by the GitHub team.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Native GitHub GUI support via GitHub Eclipse plugin
GitEye can be integrated with the GitHub Eclipse plugin to have support for GitHub.
Pro Custom commands can be defined that allow launching third-party tools
If you are using a lot of third-part tools besides GitEye, you can set up shortcuts to launch them easily from inside GitEye, greatly improving your workflow.
Pro Has a graphical compare and merge tool
Pro Great for those starting out with git
Pro Great GitHub integration
This is the official GitHub desktop client built by the GitHub team.
Pro Simple, streamlined GUI
GitHub Desktop uses an extremely simplistic two-panel view. It's not capable of complex historical visualisations like other GUIs, but it is very easy to use (especially for git novices).
Pro Supports pull requests
In addition to being able to seamlessly and easily integrate with all of GitHub's features, it also supports forking and submitting pull requests on any open source project hosted on GitHub.
Cons
Con Poor documentation
The documentation isn't very detailed and does not do a good job at explaining everything.
Con Limited
Can't handle complex tasks. The Help Manual advises to use command-line Git instead.
Con Does not support multiple Remotes for a repo
Only allowed to assign one URL as remote. To manage/sync/fetch other remotes, use command-line Git instead.
Con Overly Simplified UI
UI that is designed not to support the needs of power and enterprise users. Management of more than five repos is next to impossible.
Con Buggy
Poster child for authors' programming ideology (FRP), likely the cause for the odd quirks and bugs it has.

Con Not free/libre
This application is proprietary, and thus cannot be modified or freely distributed.
Con No Linux support
There's no Linux version of this client.
Con Non-GitHub repositories are not fully supported
Since this is mainly a GitHub client, other repositories are not fully supported and with as many features and setting up a repo hosted anywhere else but GitHub is troublesome.
