A good question, and I've written about this quite a bit. First, provide points or virtual currency that actually let you DO something with them – a good example is XBOX points that users can use to get content or add-ons. Earning virtual currency is great – but they have to have some percieved or real value. I have a ton of points with Quora and Empire Avenue that I can't "spend" because there's nothing I see there that I want to spend it on or provides me anything of "value". Use some ideas from games to "add features" that the customer can get by "cashing in" points. Provide surprises and promotions to loyal users, identifyable by session time and number of logins. Recognize your users as who they are: People.
While it's not a web app, I really like what Think Geek does. If you place an order on thier site you get Geek Points that you can spend on free stuff with your next order. Not only does that give user a tangible value (200 points equals approximately $10 worth of merchandise) but it encourages the user to place additional orders (making a casual customer into a repeat customer).
When it comes to serving the egos of your customers, I've written an article on "ego-driven design" that may be useful. You can read it here.