It really depends on the platform, but I’ve found myself partial to those that let me keep my hands on the keyboard: i3wm in Linux, and Yabai on Mac have been my favorites (although Magnet, or BetterTouchTools are also quite useful there). These allow me to quickly position and manage applications without overlap (unless desired), and to navigate around them with ease.

Virtual desktops—the 2D version, where you swap all the contents of the screen at once—have native support across all major OSes these days, so I just use whatever’s built in.