Personally I don't do any. If I am machining something from raw stock then I ensure it is positioned correctly and there is enough extra material, for bar stock I am making a height setter a bit like those used for wood routers so it is easy to make it extend the correct distance from the collet.
If I need to machine something that already exists, say for a second operation then I machine a fixture to hold it. I'm also looking at creating some sort of soft jaw system for the same sort of thing. The sacrificial plate that PocketNC sell can be used for that sort of thing too, machine some features into it and then clamp the part to it.
I also made an ER20 collet fixture that can be centered with a dti for a specific job.
Other than that some thin shim and a dowel is about the only way, someone was looking at adding a probe but it needs to be very repeatably mounted.
Cheers,
Graham