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I'm run into a frustrating problem as I'm gluing rare earth magnets to the bottom of my minis. Some of the magnets are strong enough that they overpower the super glue and come off the base. I tried to score the base and the magnet for a better bond, but no luck. The glue I'm using is Loctite super Glue gel control. Any ideas of how I can make them stay put?

Greenstuff was how I planned to do it, to give a much larger surface area for grip.

https://www.youtube.com/watch?v=NUYL7jNfZ40
Do it like this, but don't press down the magnet with your finger, instead use a flat surface, otherwise there might not be a good enough contact with your magnetic surface.
Also, take a look at "rubber steel" sheet, instead of a metal one. The bond will be strong enough to hold the magnet, but won't be too much as to tear it from your base.

1) Put a bit of green stuff
2) Press the magnet in, so that it protrudes off the bottom of the base.
3) Put some water on a smooth acrylic surface, then press the base against it, and press while doing circular motions. This will get the bottom of the magnet flush with the bottom of the base. The water will help prevent the GS sticking to the acrylic.

As mentioned, countersinking a magnet increases the surface area for potential bonding. When a magnet is bonded with CA glue on both the back and sides, you'll have a devil of a time trying to remove it, should you ever need to. I'd trust it to hold up quite well under normal use.

On flat-bottomed bases (Mantic style and most cast resin scenic bases), you can simply drill a hole. On cupped bases (GW style), you need to manufacture the supporting material "sleeve." A drilled chunk of styrene, either from thick sprue (for small diameter magnets) or laminated/very thick plasticard works and is rock solid, if bonded to the base with solvent cement. An epoxy putty blob acting like a bezel is a less labor-intensive easier option - not quite as strong, but still generally sufficient.

JB Weld or Epoxy

and as yet no-one has mentioned keying the surfaces.

For superglue to stick, it needs something to grip onto. the surface of rare earth magnets are typically very smooth, as are the undersides of bases. if you use sandpaper or (carefully) use a knife to cover the area in light scratches, the superglue will stick a lot more securely. superglue will stick to a smooth surface but it will peel off easier. it'll run into the gaps on a rough surface and get more surface-area to stick to.

this way's quicker than greenstuff, and probably cheaper too.

 some bloke wrote:
and as yet no-one has mentioned keying the surfaces.

Read the OP again. There's a reason for that.

I drill into the slotta part under the base and use that to countersink, means you can get the magnet nearer to the middle too

You might also be using stronger magnets than you need to. Remember, that if the magnet is too strong, and you simply add enough glue to hold it in place .... your figure will just separate at another point ... like the ankles.

I found that Gorilla glue works fairly well because it expands as it cures and bonds fairly well. I also echo the previous posters: you don't need super strong magnets, just using those really small ones is sufficient, especially if you have a cutout in the board for the base to set into.