Since the 0.9 Hydrogen Helix version, Payment IDs can be encrypted and embedded in a payment address. The Payment IDs of this type should be 64-bits and are encrypted with a random one-time key known only to the sender and receiver.
The Payment ID is usually used to identify transactions to merchants and exchanges: Given the intrinsic privacy features built into Monero, where a single public address is usually used for incoming transactions, the Payment ID is especially useful to tie incoming payments with user accounts.