Rules implementations that vary by rule set:

Original Revised 50th 1942 1940 Note

Bombardment casualties fire back

Subs are always preemptive Otherwise destroyers negate the surprise attack.

Air always hits subs Destroyers allow planes to hit subs.

Transports must be taken last If possible.

Aircraft Carriers take 2 hits

Notes:

Bombers as defenders are ignored in sea battles.
Destroyers in amphibious assaults are considered to have Combined Bombardment tech.
Mech infantry also get a bonus with artillery 1:1 (from 1940 FAQ).
50 edition rules heavy bombers select the highest of 2 dice rolls (from 50th Anniversary FAQ).
Must Take Territory option is ignored for sea battles.
1940s Anti-Air Gun units are ignored on the attacking side.

Info:

Order of Loss-

You may enter a string of characters as OOL.
Each unit has a hilighted letter that can be used.
If you do not enter an OOL, the default OOL will be used.
If you get an error like "OOL string is missing 'A'", it means that you have added units but you need to specify them in the OOL string as well.

Rulebook links:

General Rules Page http://www.wizards.com/default.asp?x=ah/downloads
Original http://www.wizards.com/avalonhill/rules/axis.pdf
Revised Rulebook http://www.wizards.com/avalonhill/rules/axis2004.pdf
Anniversary Edition (50th) http://www.wizards.com/AvalonHill/rules/AxAl-AnEd_Rules.pdf
50th FAQ http://harrisgamedesign.com/pdf/A&A_Anniversary_FAQ.pdf
1942 http://www.wizards.com/avalonhill/rules/AVL1942_RuleBook.pdf
1940 http://www.wizards.com/AvalonHill/rules/AVL1940_RuleBook.pdf
1940 Alpha 3 http://www.harrisgamedesign.com/phpBB3/viewtopic.php?f=40&t=6149

	Original	Revised	50th	1942	1940	Note
Bombardment casualties fire back
Subs are always preemptive						Otherwise destroyers negate the surprise attack.
Air always hits subs						Destroyers allow planes to hit subs.
Transports must be taken last						If possible.
Aircraft Carriers take 2 hits