Specialist history forums, good for discovering obscure facts.
WW2 Aircraft Forum
https://ww2aircraft.net/
12 O'Clock High - another WW2 Aircraft forum
http://forum.12oclockhigh.net/index.php
Warbirds Forum - another WW2 Aircraft forum
http://www.warbirdsforum.com/
Axis History Forum - Good for information on minor Axis allies, as well as Germany, Japan and Italy.
http://forum.axishistory.com/
WW2 Weapons
http://ww2-weapons.com/
WW2 In Color - Mostly a picture site, but good for getting a sense of what airbases looked like, possibly exactly what equipment was used.
http://www.ww2incolor.com
WW2 Database
http://ww2db.com/index.php
History of War - Not as well indexed as it could be, but a good source for general unit and campaign histories, as well as equipment.
http://www.historyofwar.org/index.html
Hyperwar: Hypertext History of the Second World War - military manuals, orders of battle, official histories, etc. but mostly from a US perspective.
http://www.ibiblio.org/hyperwar/
Aeroflight - A comprehensive aviation site which covers both current and historical aviation around the world. It's a good starting place for information about historical air forces, airfields, aircraft, etc.
http://www.aeroflight.co.uk/
For Minor Air Force Orders of Battle, including some obscure info, this site is quite good. It's also good for potential scenarios, since it was created by a wargamer for a tabletop air war game.
WW2 Minor Power Air Forces
http://world.std.com/~Ted7/minoraf.htm
WW2 Ace Stories - Collection of stories about aces of all nations.
http://www.acestory.elknet.pl/
Air Aces - a comprehensive list of Aerial victories, sorted by nation, Air force, war, etc. Good for pilot pictures, units, etc.
http://aces.safarikovi.org/
Aces of WW2 - another Ace site, but less comprehensive than the one above.
http://acesofww2.com/
Air Aces Homepage - yet another Ace site
http://users.accesscomm.ca/magnusfamily/airaces1.htm
For Finnish AF Ops, this site is quite good. Some articles are in English, otherwise Google Translate is "sort of" your friend.
http://www.virtualpilots.fi/
For Regia Aeronautica
Stormo!
http://www.stormomagazine.com/
Aerei della Regia Aeronatica
http://www.finn.it/regia/
Commando Supremo - Italy at War
http://www.comandosupremo.com/regiaaeronautica.html
Hakans Aviation Page - Biplane Fighter Aces from the Second World War - Also good for Finnish, Hungarian, and Chinese - basically any AF which used the Gloster Gladiator and/or the Cr.42.
http://surfcity.kund.dalnet.se/
Excellent Luftwaffe site, which sort of helps with Minor European Axis Nations.
The Luftwaffe 1933-45
http://www.ww2.dk/
For France:
France 1940 - mostly Battle of France, but some later war stuff
http://france1940.free.fr/
For Japan:
Nihon Kaigun - Imperial Japanese Combined Fleet - For Japan - especially the IJN
http://www.combinedfleet.com/
J-Aircraft - anything related to Japanese aircraft
http://www.j-aircraft.com/
VVS:
VVS Research Page
http://mig3.sovietwarplanes.com/
War Is Over - Aviation in WW2 - Also click on Russian version of the page and use Google Translate to try to get more info.
http://www.wio.ru/ww2a.htm
Lend-Lease Air Force - US and UK Lend-Lease Aircraft used on the Eastern Front. Also click on Russian version of the page and use Google Translate for more info.
http://lend-lease.airforce.ru/english/index.htm
War By Air Force - An IL2 server site with some good historical articles.
http://war.by-airforce.com/index.html