[jwr]

Good advice, except for debugging (SWD). For that I would definitely go with Tag-Connect (see my article at https://partsbox.io/blog/choosing-a-debug-programming-connec...). Main reasons: 1) my boards are space-limited, 2) I really enjoy using a single debug connector for all my boards (and many third-party boards as well), 3) I really like the idea of having a debug connector that costs $0 on the board.

As for other connectors: for Li-Ion batteries I use JST-PH connectors, standardizing on the pinout used by AdaFruit for batteries they sell.

For any custom "future extension" type connectors with I2C or SPI: 0.1" header holes. I can use them to either solder wires or place pin headers if needed.