I went with $3.99 because Prowl is $2.99 and Notify My Android is $3.99. I'm not convinced that a yearly service is worth the overhead and I personally wouldn't pay to use a notification app that had a yearly fee.
The bandwidth and server overhead for running such a service are pretty low and iOS/Android push notifications are free, so I'm not really worried about monthly costs for normal users outweighing the revenue the app brings in. Right now Pushover is running on one of my servers that does other things, so it's not even really costing anything tangible. If costs start to go up, I can always increase the price of the apps to slow growth (or increase revenue if it doesn't slow growth).