When comparing Tower vs GitHub Desktop, the Slant community recommends Tower for most people. In the question“What are the best Git clients for Windows?” Tower is ranked 13th while GitHub Desktop is ranked 17th. The most important reason people chose Tower is:
Tower has a good-looking interface and consists of 3 main views - services, repositories and repository. - Services view for managing integrations with hosting services like GitHub, Bitbucket and Beanstalk. - Repositories view for organizing local and remote repositories into folders and getting general overview about them. - Repo view that consists of two main subviews: - Working copy view shows modified files and their diff and allows wrapping up changes in a commit. - History shows commits alongside metadata and projects file structure. Additionally, it allows performing various tasks such as merging branches via drag & drop, search allows searching by message, commit hash, author, committer and file and there's a quick open that allows fuzzy-searching for folder names.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Pretty, modern-looking user interface
Tower has a good-looking interface and consists of 3 main views - services, repositories and repository.
Services view for managing integrations with hosting services like GitHub, Bitbucket and Beanstalk.
Repositories view for organizing local and remote repositories into folders and getting general overview about them.
Repo view that consists of two main subviews:
Working copy view shows modified files and their diff and allows wrapping up changes in a commit.
History shows commits alongside metadata and projects file structure.
Additionally, it allows performing various tasks such as merging branches via drag & drop, search allows searching by message, commit hash, author, committer and file and there's a quick open that allows fuzzy-searching for folder names.
Pro Offers a visual way to solve conflicts
Tower shows conflicting files, their authors and the commit that made changes. It then allows selecting which files should be used in the final result.
Pro Github integration
Pro Very polished user interface
Pro Cherry-Picking via drag and drop
Pro Git LFS
Tower comes with built-in support for Git LFS. Handy when working with large files.
Pro Git-flow integration
Git-flow provide a consistent development process by defining a strict branching model that is great for managing large projects. T2 allows setting up and integrating into repos that follow this model.
Pro The UI only shows the needed commands at a time
Tower covers most of the daily tasks that a developer may need to complete. It shows only what you need for the most common tasks without overwhelming the user.
Pro Free for students
If you are a student, you can get your free Tower Pro license here.
Pro Interactive Rebase via Drag and Drop
Pro Undo Support
Many Git actions can be undone in Tower simply by using the keyboard shortcut CMD+Z. Examples: Deleting branches and files, staging changes, rebasing & merging branches, or publishing a branch on a remote
Pro GPG support
Tower offers user profiles. You can then connect GPG keys with your profiles, sign commits and see which commits have been signed and by who.
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 Not free/libre
This application is proprietary, and thus cannot be modified or freely distributed.
Con Expensive
Costs $69 per year!
Con Inefficient UI
In order to not overwhelm the users with information, much of the information is either hidden by default or requires navigating to a different section to access.
Con Doesn't have a built in diff
Con Stability issues on Windows
On a simple repository, the UI often lags or freezes.
Con Doesn't support Subtrees
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.
