Xenonauts is pretty good, I definitely recommend it. Even if I haven't played it as much as I should.

While I am sure similar software already exists, I spent most of today on creating a small utility that would allow you to very easily put down small notes about what you've been working on and outputting them in JSON, so it would be uploadable to a web server to track time.

Unfortunately I am not well versed enough in AutoHotkey to give you a good answer, but from what I've seen... probably? But it would take a lot more code to accomplish what AutoHotkey can accomplish with a page of script using C#. From what I gather AutoHotkey has a pretty narrow scope (Feel free to correct me here, AutoHotkey gods) of what it sets out to accomplish, and does this extremely well. That scope entailing automation of tasks and small simple UIs to facilitate this, an example being renaming files or doing specific tasks at different times. Whereas C# is designed to be a fairly high level multi paradigm language that you can use for pretty much anything.