Presumably this regulation will affect all of the other payments companies in this space. (e.g., WePay, Venmo, Dwolla etc). It would be interesting to hear their thoughts on this.
http://www.quora.com/Does-WePay-have-a-money-transmitter-lic...
Aaron himself says Square isn't a money transmitter:
http://www.quora.com/Square-company/Will-Square-be-subject-t...
Payment processors are regulated differently than money transmitters:
The money transmitter definition also provides that “the acceptance and transmission of funds as an integral part of the execution and settlement of a transaction other than the funds transmission itself ... will not cause a person to be a money transmitter.”
[...]
FinCEN has already concluded that a merchant payment processor acting exclusively on behalf of merchants receiving payments for goods and services, rather than on behalf of consumers making payments to merchants, is not a money transmitter.
Venmo doesn't have any licenses to the best of my knowledge. Maybe they're an agent of someone, too.
Dwolla thinks that they're exempt but I'm not entirely sure that's true. They have a credit union service provider as one of their investors, but that's not necessarily the same as being an agent of a federally chartered bank or credit union.
Noca, Xipwire, Cimbal, LendingKarma, KoolWallet and others are affected as well.