Visitors are frequently sent to the same advertiser via multiple publishers. Last Cookie Counts means that the publisher who last forwarded the visitor receives the commission from a transaction. The term Last Cookie Counts refers to the fact that many advertisers use cookies to determine through which network the visitor was last forwarded. Another term for Last Cookie Counts is Last Click Counts.
If an advertiser has an affiliate program with multiple affiliate networks, then it's possible to setup a script for so called 'network deduplication'. This prevents transactions from being registered with multiple
networks.
Last Cookie Counts is often abbreviated to LCC. Read how to implement the LCC method here.