APIS is a CBP database required for flights departing/arriving internationally. Commercial aviation has been, for quite some time, required to provide CBP with passenger name and travel document (ie Passport) information electronically a minimum of 60 minutes prior to departure and receive permission from the DHS/CBP to depart the country. In theory the CBP is matching the passenger/crew manifest to a secret terror watch list and will forbid the departure with the people who's names are on the list. Same with international arrivals.
In essence, the airline is required to transmit to CBP computers a list of who's on the aircraft (crew and pax) and get permission to depart from or return to the US. CBP will then decide if it will allow those passengers to freely travel across our border. I think this is part of the rationale requiring everyone to have a passport under the "Western Hemisphere Travel Initiative."
It is one more way that DHS and its subsidiary agencies can keep track of U.S. citizens and others who wish to leave or enter the country. It amounts to an exit visa.
This was extended to private aircraft about 2 years ago and requires internet access to file the inbound/outbound manifests of both passengers and pilots. The current procedure is to file the information electronically and wait until you receive an email message from CBP saying you can depart for a foreign airport or a US airport. CBP has used this information to detain at gunpoint at least one aircraft in southern California departing to or returning from Baja California. (See the Baja Pilots Assn. web site for more details on this).
DHS's CBP commercial web site
here has more information and for private boats and airplanes,
here. A password is required to look at the documents and CBP has posted that password on the site. I have not read these documents, but since I operate private seaplanes in/out of remote lakes in Canada, this program has been a nightmare for me personally. Last time I was at N53.56 W92.94, there was no internet service. Come to think of it, the four of us and fish were all that were there. Nappy has publicly stated she is planning to expand this to pleasure boats in the future. More information
here.