I've had some good results using acrylic paint. Gouache is good too if you keep it somewhat thick, and put a coat of fixative on afterwards, although the glossy surface of the cards makes it somewhat difficult. I generally use some combination of acrylic/colored pencil or acrylic/gouache.
As to warping or any destruction of the cards, not really an issue for me. Most of the customizing I do is making custom proxies. My process is taping down the cards along the black border to a rigid surface. Then I remove the ink with acetone, while still preserving the black border. Then I do the drawing. Once the drawing is finished, I go outside and spray on fixative, then once it's dried, I apply a layer of acrylic matte medium to really seal the drawing in. Then I just paint away, and apply another layer of matte medium when I'm finished to seal the painting. Keep in mind, that since the magic cards are meant to be water repellent, that the paint doesn't bond very well with the cards, but is more or less on top of the cards, so be careful not to let the paint peel up off the card. I hope I helped, good luck.
Straight Acrylic paint and fixative, though I wouldn't play the cards without card sleeves.
edit: nofingers describes it pretty well, though I should mention putting acetone on your card will strip the original layer, you'll be working on a straight white space while keeping the original card back. I've seen Magic artists just paint over the card, I have a couple but I don't play with them.
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yeah that's great. Since mtg cards are fairly water resident on the front...what if you made small cuts using an exato knife or box cutter does that work or ruin it.
P.s. thanks for the web links even though there not paint it's cool. I'm just trying to mess around with a Torchling...you know how we've seen a morphling turned into a stormtrooper ect. ect. That what i'm looking to do. It looks like paint that they use not markers...anyway cool. Thanks