I think the key is to expand your exposure inside the niche that you're exploiting. I know, that sounds really bad, but wait, let me explain. Of the number of views you receive, if your ads are well targeted, a certain percentage will sub. The higher the percentage of subs the better targeted your ads are. So, I wouldn't just run ads, but several ads that target several different types of readers. By referrer you can determine who best to target, and which ads are most effective inside that niche. Finding the readers who are most likely to stay and interact with the comic is the tricky part, and it's something I haven't mastered, so any ideas that you can share as well are helpful.
I think, though, interaction is key. Anything you can do to get them to invest in the comic will get them to return, and draw more readership. So, it's cliffhangers, and sequential jokes that build over several pages. Anything you can do to randomly reinforce a return is a good thing, I think. It's like operant conditioning.
If one thinks of the way games are designed, it's much the same. They reinforce behaviors through a system of rewards on an ever increasing but random schedule. The best games do this and consequently have the largest following. This is not by accident. A great deal of effort goes into designing a reward schedule that serves the subscription needs of the game. It's how the good ones continue to make money long after their initial release.
One thing I've seen a few artists do is break the fourth wall to thank readers and subbers explicitly. I'm planning on using this tactic at the most opportune moment. I just haven't decided what that moment is.
I would be more than glad to hear of any strategies that you find that work.