Sadly I was great at making things easy to use, I was great at making new features, I had no problems getting into things like Twiistup and being nominated for the Webware 100, etc... but making money I am not good at. For example I had a two year head start on Basecamp and they are living high on the hog and I am just barely living :) I had to just abandon the crm (I just cut off the signups but all of the old users are on it still using it) and I am going in a new direction.
Have you tried simply charging for it ? Put in a pricing grid with the corresponding app restrictions. Of course, grandfather in all existing user to a free tier with a generous grace period. The free tier may or may not accessible to new signups. Call it the "end of beta".
Seriously, try it. You obviously are providing value to users. I'd love to hear from you on how it goes.
I have been thinking about making everything super encrypted and charging $100 a month. I have had a number of defense contractors come and try it but not use it because I could see their data. Then I wouldn't need to upgrade the interface which is a bit aged. But I am burned out right now, maybe in 6 months. The current users, I hit them up for some donations but I attracted people who don't really want to pay.