Is there a way to re-order the custom filters?

That would be very nice.

At the moment, since I created the filters as needed, they are in a somewhat random order and it would be neater to have, say, all colour filters next to each other, all list filters, and so on.

I look into this.

For now, you can edit the CustomFilter.plist in Application Support/Glyphs. Restart Glyphs to see the effect.

Thanks! CustomFilter.plist did the trick.