I use API's from 3 different sites: DogeAPI.com, for doge payments, LiteAPI.org for Litecoin, and Blockchain.info for Bitcoin payments.

LiteAPI, and Blockchain, are great as they have callbacks (and are virtually identical), for DogeAPI I use EventMachine (Ruby) to poll DogeAPI to see if payment has been received.

My store is a custom version of Potionstore (Ruby on Rails): https://github.com/potionfactory/potionstore