The payment methods used by the various advertising networks and affiliate programs depends to a large extent on the country in which the ad network operators are based and also their publishers.
Most US based affiliate programs and ad networks offer payment through Check, Paypal. Some also offer direct deposit in the bank account for US based publishers. For international publishers, direct deposit is available on payment of an additional fee.
Moneybookers is a popular money transfer system in Europe and has low fees compared to Paypal. It allows transfer of funds to bank accounts.
Compared to Paypal, Alertpay is new, but allows check withdrawal and wire transfer for a fee.
Liberty Reserve, Perfect Money, WebMoney and ePassporte are some of the other payment methods offered by Advertising Networks.