"Fact is, Facebook is only making so much money because Microsoft entered into an agreement with them guaranteeing them profits per year. You as an independent developer will get even crappier CTRs."

One huge reason why I suspect Facebook's click through rates are so low is because they actually respect their users by not putting their ads in annoying, profitable places. As an Facebook app developer, you probably have far fewer users than Facebook, so you don't have the luxury of making up the costs of respect with volume. If you put your ads in more annoying places than Facebook does without being annoying enough for people to stop using your app, you can probably make money. The Graffiti app does this on their canvas pages with AdSense. I'd like to see their numbers.

Or you could actually do a good job of advertising instead of silly lowest common denominator ads. As a Facebook Platform app, you have access to quite a bit of data about your users. Use it. To do a good job of it, you'd probably have to sell your own ads. Then you could ask yourself if each ad will actually be useful to your users, and reject them if they're not. Whether or not that would be a profitable endeavor is left as an exercise for the reader.

The other option is to provide a useful service to your users that results in them paying you money. Very 20th century, I know. iLike seems to be doing a pretty good job of it.