I was originally going to use 3.5mm audio jack (like maverick and most meat probes) however. There is a lot of durability and signal problems associated with this. One of the biggest is that thermocouple wire cannot be soldered, only welded.
With this in mind. I am using industry standard Mini Thermocouple Jacks. Now the good and bad...
Good: Industry standard connector, Easy to fix if damaged. If you want a different type of probe that I do not carry you can go out and but it. It will work fine with my controller.
Bad: Connectors are expensive! Almost $4/each for PCB connectors. However the wire connectors are MUCH cheaper <$1
I feel the trade offs are worth it for the better performance