There are tons of people that hate AdFly, and for some reasons, I am one of them. But I'm going to start using it on my website and see how you guys feel about that. There will always be a Direct Link too, but AdFly is probably the best way to earn money at the moment.
But what about annoying pop-ups?
For my peeps on Firefox and Chrome, you can download a popup blocker and use that, but keep your adblocker disabled. This works great for AdFly. Otherwise, you can just stop being a lazy douchebag and click the close button.
Where will you put them?
On the Download Pages mainly, but you may see the occasional one on the homepage.
What about other ways of earning money?
Like AdSense? Well, that requires all sorts of fancy crap, and AdFly is way easier to use. However I might put AdSense on the website in some places.