Today, even a small website project has a lot of dependencies and it's fitted into a workflow of some kind. Here are some tools we're using every day bar the obvious ones (email, Photoshop, etc).
Once the project is underway, this is what we use for tracking hours spent on it. It's a browser application with plenty of useful features even if you don't go for the pro version. Some of the interface solutions are a bit awkward but you'll get used to it quickly. Check this post for a nice comprehensive review and useful tips.
We only needed Photoshop and Illustrator from Adobe. This wasn't feasible so enter Affinity Designer. So far it's been doing a good job filling quite a big pair of boots. Sure, it lacks some features but at least for our fairly modest needs it's a good solution.
Flexible, flexible, flexible.
Even though we're shifting to ProcessWire, WordPress is still our number one tool for blogs.
De facto version management and also an essential part of our project management.
A proper text editor saves countless working hours in the long run. Atom is intuitive and has a great community that constantly produces plugins for everything you can possibly want.
Sass is CSS on steroids and amphetamine - without any nasty side effects. It extends CSS syntax to great lengths with nested styles, variables, mixins and so much more. You can hook it up with very useful task runners such as autoprefixer to streamline your workflow even further.
Good coffee just makes everything better.