Links, sorry about the lack of descriptions/organization, it's on my "to do" list.
www.ptboats.org, dedicated to the preservation of PT boats and host of the best PT boat forum in the world.
http://geocities.com/pt_king/PTboats.html PT King, reference site with great images.
2009 update: The above site has been revamped and moved here (geocities sites will be closing soon): http://pt-king.gdinc.com. Richard Washichek is graciously hosting it, check here for neat PT drawings of his: http://gdinc.com. Dick also administrates the forum at ptboats.org.
http://www.hnsa.org/doc/ Navy manuals including ordnance like the 20mm, 40mm, and depth charge.
http://www.hnsa.org/doc/pt/doctrine/, Motor Torpedo Boats, Tactical Orders and Doctrine, July 1942
http://www.hnsa.org/doc/pt/specs/, Detail Specifications For Building Motor Torpedo Boats, March 1944
http://www.ibiblio.org/hyperwar/USN/ Great reference site by Patrick Clancey
http://www.ibiblio.org/hyperwar/USN/ref/PT-Manual/ Motor Torpedo Boat Manual, February 1943
http://www.ibiblio.org/hyperwar/USN/CloseQuarters/index.html At Close Quarters, PT Boats in the United States Navy by Captain Robert J. Bulkley, Jr., USNR (Retired)
http://www.ibiblio.org/hyperwar/USN/ref/MG/index.html The Machine Gun. History, Evolution, and Development of Manual, Automatic, and Airborne Repeating Weapons by George M. Chinn, Lieutenant Colonel, USMC
http://www.navsource.org, NavSource Naval History, Photographic History Of The U.S. Navy and a great reference site.
http://www.navsource.org/archives/12/05idx.htm, Patrol, Gunboat, Submarine Chaser and Section Patrol Craft Index. Photos of different PT boats.
www.history.navy.mil PT 109
Louisiana Library Higgins Blueprints
Some interesting PT info including famous crewmen
Great story by Dick Keresey
pistolpackinmama.net, site dedicated to a grandfathers service on PTs 209 and 243
Researcher@Large Many Ships-2 update memos and instructions as well as other historical documents.