I've done two different methods. The first is to use brass rod (1/16" or 1.5mm) drilled into a plastic GW flying base and permanently glued into a matching hole drilled into the base of the vehicle. This was used for the elder skimmers and jet bikes. The marine speeders also used brass rod, but were mounted with green stuff to a 3/4" flat washer instead of the larger plastic base.
viewtopic.php?p=483354#p483354viewtopic.php?p=483357#p483357More recently, I've done some removable bases using 1/8" or 3/16" diameter magnets, so I can separate the bases for storage or re-use a pool of common magnetic bases across different vehicles. The base is a 1.25" fender washer with a square of plasticard (1mm - 1.5mm thick) super-glued over the hole. Then a hole (1/8"?) was drilled through the plasticard to match a GW flying base stalk (I have a lot left over in my bits box), this is then glued into the hole with plastic cement for a nice strong bond. The stalk is then cut down to around 10mm in height, and sanded flat on top. A magnet is glued to the top of the stalk. A matching magnet is glued to the bottoms of vehicles, either drill a shallow hole to match the depth of the magnet for a flush fit, or use a blob of green-stuff around it to mount securely.
I like the look of the brass rod, but the thicker plastic stalk is better for mounting magnets, and I think a little more useful in the long run.