So far the cabling system consists of 2, 4, and 10 wire cables. I have considered  adding a 6-wire cable for SPI, but the 10-wire will suffice for that. I'm trying to avoid creating a need to stock more different parts, and the 10-wire connectors are small enough (and wires don't need to be stuffed if not needed). The connectors can all be JST PH, with a 2mm pitch. 

However, the 4-pin cable I prefer is Grove ie Seeed Studio's standard cable, which also has a 2mm pitch. These can be purchased from Digikey so are easy to come by. They are good for I2C, serial, LED strips, quadrature encoders...anything requiring two wires...and also GPIOs, analog, and so on.

The 2-pin cable is a JST PH. I am using these for contact closure, LED outputs, speakers, etc.  Some PH cables can be purchased on Aliexpress, but as I wanted a variety of lengths, I found a supplier using Alibaba and ordered several hundred direct from the factory. 

The 10-pin is a JST PH. Its 8 signal lines, power, and ground. A board is available to convert this to a 0.1" pitch Dupont style connector. The 10-pin Dupont cables were purchased from Aliexpress. I'm finding the 10-pin to be useful for consolidating several of the smaller connectors into a byte.

All three styles of connector shell have a plastic tab holding each wire, and its easy to temporarily bend up the tab, release the wire, then put it back in different position or different connector shell. I find this very useful. I've not had good luck with connectors that have a metal retaining tab. 

If you use PH through out, then it is easy to move the wires around between different width connector shells.  One might just as well buy the crimped wires without the shells, and put them in the shells as needed. The PH has a slightly lower profile then the Grove, which helps as space in an enclosure is often a problem.

But the colour coding of Grove is helpful, the cables are easy to come by, and there are a variety of companies offering products using Grove. For instance, Sparkfun's I2C system, QWIIC, has a Grove adapter cable, so bridging into that system is easy. Moving wires on a Grove connector is easier than on a PH.

I think generally the boards are best to have unstuffed (ie not pre-assembled). Yes that breaks the solderless concept. In practice I'm finding 1. the boards are so simple they solder together in minutes and 2. there are a variety of ways to put together a board eg using right angle vs straight connectors, male vs female, putting connectors on the other side of the board etc. Since the Grove and the PH have the same footprint, the user can make that choice when assembling. Then for instance one could bridge into STEMMA or DFRobot Gravity,  which use the JST PH as well. 

A note regarding the connector orientation on the boards: the polarization slots should point inward, to allow for right angle or straight connectors to be used. Right angles always have the slot on the top.