I have used many Linux boxes and set up many servers. When a new Linux box is up, I install some necessary apps. The detailed installation on Linux is up to your flavour, but I will list some apps that will tell you how your system is up and running and manage some configuration files.

Htop

I am a big fan of Htop, even if the system has Top as built-in. Htop has nothing more features than Top, except visual CPU, memory and Swap indicator.
The main difference will make me understand more about my system and let me know which process is working so hard on each request.

emerge --ask htop

Iftop

Iftop is the app I install every time to check the response rate. As a web developer, I want to see how the system responds to each request. You can test with Lighthouse or a webpage speed test, but I need to know how fast my system responds to clients in real-time.

IOtop

IOtop can help you analyse where your system is stuck. When the response time is high, it can be because of both app response and system delay. You can check how your system loads and unloads files from one drive to another.

VNstat

I installed VNstat even when I installed Iftop. I have to read the data transferred by day or by month.

Vim or Nano

I install only one. Vim is an advanced text editor, while Nano is a minimalist text editor. If you are familiar with Control Key, Nano is your friend. Otherwise, Vim is your love.

Screen

The screen is the only choice if I want to manage multiple screens inside the terminal or the server.

The screen can split the console vertically or horizontally with ease.

If you have installed the above apps, it is up to you. You can manage your box for more apps.