I see someone suggested Beeminder in the comments of your post (thank you, whoever that was!). Also by the creators of Beeminder (me and Bethany Soule) is TagTime, which is related to your idea of periodic prompts. We call TagTime "stochastic self-sampling" or "time-tracking for space cadets". It's not super friendly (a huge pain to get working on Windows, for example) but it's on github here: http://tagti.me

If you don't want to deal with TagTime (and I don't blame you) then just hooking up RescueTime to Beeminder is a great way to go. Here's what RescueTime says about Beeminder:

http://blog.rescuetime.com/2012/11/27/give-your-productivity...