When comparing GitExtensions vs GitHub Desktop, the Slant community recommends GitExtensions for most people. In the question“What are the best Git clients for Windows?” GitExtensions is ranked 7th while GitHub Desktop is ranked 17th. The most important reason people chose GitExtensions is:
It's totally free And its written and thought by developers who really know what you need as a developer. Open to contributions by everybody.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Open source
It's totally free
And its written and thought by developers who really know what you need as a developer. Open to contributions by everybody.
Pro Git commands visibility
GitExtensions typically displays all commands that it carries out in a separate window. The user can also open the Gitcommand log (under Tools) and view the git commands as they interact with the program.
Pro SSH support
Instead of using HTTPS and authenticating every time they are pushing their code remotely, plenty of developers prefer to use SSH to communicate with the remote server and authenticate using secure key pairs.
Pro Powerful commit screen
Staging/unstaging files and/or lines of code, ammending, overriding commit's author, commit templates.
Pro Many advanced features made easier to use
Complex git commands such as resolving a rebase conflict or performing a subtree merge are made much easier by a helpful UI.

Pro Great UI
GitExtensions has a simple layout, all usual functions being available without navigation menus. The branching and merging are clear and easy to follow.

Pro Lightweight and fast
GitExtensions is a lightweight and fast application.
Pro Very good stash support
Easy to save, view & pop stashes.

Pro Easy to set up
Can either be set up as a shell extension, standalone tool of Visual Studio plugin, allowing developers to choose the way that suits their workflow best and is easier for them to get into.

Pro Easy to use
Can be used as a Visual Studio plugin for developers who use it as their IDE, or as a standalone tool. Both are easy to use even for users not very familiar with git.
Pro Submodule support
Powerful submodule support, also when working with multiple cloned SuperRepos.
Pro Responsiveness
Pro Useful plugins
Includes Gitflow, also has a delete obsolete branches feature which is very useful to get rid of those old branches that have already been merged. There are also other options to clean overall clutter in repositories.
Pro Built-in git-bash console
This makes running custom git commands quicker.
Pro Eases initial git configuration
The settings window on first run helps you set lots of required settings such as your commit email address.
Pro Simple global / local diff and merge support
Makes working with repos using different languages and support tools much easier.
Pro Allows easy setting up of scripts to enhance productivity
Pro Plugin API
There are several out-of-the-box plugins installed with standard setup. Additional behavior customization is possible with new plugins (written in C#).
Pro Integration with common tools like Jira or TeamCity
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 No side-by-side diff
There is no option to do side-by-side review of files. Creator(s) do not feel this is a desirable feature. While this is great software in almost all aspects, not giving the end-user a choice of side-by-side diff (inside GitExtensions) is a deal-breaker.
And no, using an external tool to do this is too much of a hassle, because of the amount of files to check in each change-set (in my case that are often 200 to 300 files).
Con Not truly cross-platform
GitExtensions is not truly cross-platform. It can run through mono on UNIX-based systems but this does not work as well as it does on Windows.
Con Missing tabs to have more repositories open at once
Con Doesn't offer " Repo Groups"
Repo groups (best done in smart git, Git Kraken's version is also decent) is an amazing time saving feature when you work with multiple repos on a daily basis. This is the only con!
Con UI does not render properly on Windows 10 x64
Con UI may feel cluttered with too much information
The sheer amount of information that the UI displays by default may feel overwhelming at times, if not outright confusing.
Con Linux version has no updates
If you want an updated version, you have to download the source and figure out how to build it yourself. Developers don't have any kind of documentation or faq about this process.
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.
