There are such fabulous cupcake papers out there now. But after baking, you can't even tell what the paper is. Is there any way to have clear and colorful papers on the cupcake after the baking? HELP!!

You could try cupcake wrappers:

http://cakecentral.com/modules.php?name=gallery&meta=search&type=full&search=wrappers&album=121&search_user=

HTH

I always bake my cupcakes in plain white liners or the unbleached light brown ones. After decorating I drop a dot of icing in the bottom of a fancy/colored cupcake paper or if it is for a special occasion into a hand cut cupcake wrapper.
You are right the design does not show up if the cupcake is baked in it, especially the dark chocolate cupcakes.

They make grease resistant cupcake papers now, if you use them the design is as pretty after baking as it was before. the wilton ones are not grease resistant: I got mine (reynolds brand) at a grocery store. Quite a bit more expensive but really perfect: its an inner foil lining that keeps them pretty. Much more appetizing imo.

I just made cupcakes using liners from michaels and you can still tell they are pink with white polka dots. I made dark chocolate cupcakes too.

FYI-I was in Michael's yesterday and they were having a sale on many of the cupcake papers-99 cents. Stocked up on the cute ones.

Here's an image of the cupcakes I made last night: the black and white one is a grease resistant wrapper, and the blue ones (though you can barely tell they're blue) are the kind from Michaels.

Edit: I can't get the image to attach. If you're curious I'll upload it to my photos, its another view of the football cupcake.