My application manages and measures data (like visits, social activity) around a specific type of web page. The data doesn't really get interesting until you have a corpus of 4 or 5 different pages in the tool. For some users this process could take a month. How can I keep users interested, and not disheartened by flat lines and sparse tables, whilst they on-board?
Honestly, when there's nothing for them to do, keeping their engagement is going to be an uphill battle. For me, when signing up for these kinds of tools, what helps the most is getting an email when there IS enough data. Odds are, I've forgotten I signed up and wandered off, and getting notification that there's now something worth looking at is often enough to draw me back and cause me to become more engaged with the product.
When reading your question, I immediately thought about the web app "RescueTime". It track the time you spend on your computer so you can quickly see how productive you are. Even if you recorded only some minutes, the design has been made so you don't feel like it's empty.
If collecting data takes time then let them do something else but keep doing your work and then, depending on how much time you need to give usefull informations, send them an email.