The payment system of our pool is PPLNS: whenever a block is found, payment is given to shares submitted in a window, starting with the last share submitted and going backwards up to some number N of shares. Shares older than the window are not paid.
We use a shift system to collate the shares submitted, and our PPLNS reward is calculated from the last 10 shifts. This is the same for altcoins which are being merge mined by the Bitcoin pool, and Scrypt coins, which are mined in a separate pool.