When comparing GitHub Desktop vs gitk, 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 gitk is ranked 26th. The most important reason people chose GitHub Desktop is:
This is the official GitHub desktop client built by the GitHub team.
Ranked in these QuestionsQuestion Ranking
Pros
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.
Pro Visibly more compact overview output than many other options
When using gitk to scan a long list of changes, the user is able to see more of the list without pagination, as there is no huge buffer of whitespace between each entry.
Pro Fast
Since it's pretty minimalistic and does not contain a lot of features (for example, it can't commit), it's quite fast.
Pro Free
Gitk is a free and open source tool. It forms part of the official git suite.
Pro Comes with Git
Gitk is a part of the git package, so no additional application is necessary: it is developed right alongside git itself.
Pro Easy to use
Cons
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.
Con Cannot commit
The user needs to use a different Git client (GUI or otherwise) to commit changes.
Con Does not automatically update
The user must press F5 to refresh the view as there is no automatic update available.
