The way I see it, while you don't wield as much power over the frothing masses as Gabe and Tycho, you still have a considerable amount of influence over a relatively large number of people, DJP. Given these conditions, you really need to consider what your priorities are. Before you start talking about ditching Child's Play for a medical charity, you need to at least come up with a set of diseases you might consider fighting, there are a lot, and at times it seems overwhelming. And in the end, by choosing a narrow set medical charity, you've essentially swapped a minor benefit to a wide group of kids for a major benefit to a much smaller group of kids. Your donations might have made a breakthrough in the fight against Cystic Fibrosis, but now there are kids with ALS who don't even get a game to pass the time before they die. Such are the choices one must make.
But here's what I want to know. Why do you need to make a choice right now? You seem like you haven't figured out what charity you would like to go with from a medical standpoint, and even once you make a decision, there are still issues to tackle on the logistics of paypaling the donations and setting up the banners, and that'll take a little more time. But in the interim, it sounds like Darkesword already has an idea for how to set up the CP donations. Why not do both? There's room on the page, especially below the Firefox with Google Toolbar! ad on the siderbar. If I was in your position, I'd slap the CP link right there, right now, and think about what medical charity I'd want to add. Get the donations flowing to a charity now, rather than waiting for the ideal charity, in the end, the donations that could have been made today won't detract alot from the donations that will be made when whatever additional charity pops up. You could even compile a list of medical charities you like, then have the community vote on which one they're more likely to donate to, and throw the winner up there to replace the CP link. Or you could leave the CP link up there alongside it, as I said, there's plenty of room for another good cause.
*sigh* I go to all that work, just to have you come up with the exact same idea while I was typing...