When we did this for our own company we implemented in house, but we were at a high level of execution and resources (<100 employees).

If you are small I'd recommend http://www.referralcandy.com/. It's a very simple system that you can implement and the payment tiers let you get it fairly "invisible" if you so desire.

Some of those built their own in-house. But some platforms that many companies use are: Rewardstream, Referral Saasquatch, Referral Candy, and Amplifinity.