alea tools has magnets of different colors made just for miniatures. They work pretty good, until you get a couple guys next to each other that each have a magnet or two on them, then invariably you go to move one guy and all the magnets fly together. the way around this is to glue these magnetic bases to your minis, but they only give you like 20 and that aint enough to cover my mini collection by far, but even if they gave me enough I wouldnt want to take the time to do it, especially since the bases are 1 square inch, so they only stick to the bottom rim of the minis, which means they fall off somewhat easily. Unless of course you want to take the time to cut them all to fit inside said rim...
I started using colored paper clips, but when I was at gencon I demo'd pathfinder and they had little squares with different conditions written on them that you put underneath your minis, they looked nice, haven't played 4e in a while though (because of all these little issues) so not sure how well they would crossover.