I just published Zen Cart Reward Points, a new mod that allows stores to assign loyalty points to transactions, which can be redeemed later for merchandise. Unlike discounts, which reduce the bottom line right away, reward points offer a way to incentivize customers to stay with you, but deferred the costs.
The Reward Points mod is a custom software installation, configured according to your request. One of the implementation models involves using Frequency Discounts to compute reward points, so a customer would only earn reward points if purchases exceed a certain amount during a specific look-back window (say 90 days or 1 year).
Other implementation models are possible; just let me know your needs.