Here is a start on the reference section that deals with cockpit and well colors. I'm sure there are many errors so I would appreciate any inputs. Please provide references if you have them. Also remember that this is just a basic primer (no pun intended) and not intended as the final word on the subject.

NOTE: Colors given are the primary ones. Naturally with cockpits there are a number of other colors for things like instrument panels, seats and other equipment. Same for equipment in gear wells.

 
Aircraft Subtype Cockpit Wheel wells Struts Inner Gear Doors Misc References
A-10 Warthog All Dark Gull Grey White White or Light Grey White Wheels could be white or light grey
 
Bf-109 B/C/E RLM 02 RLM 02 RLM 02 RLM 02 Some late E's interior RLM 66
 
Bf-109 F/early G RLM 66 RLM 02 RLM 02 RLM 02 Some early F's interior RLM 02
 
Bf-109 late G/K RLM 66 RLM 02 or underside color RLM 02 or Aluminum RLM 02 or underside color Some G-10/14 had red struts/wheels
 
Bf-110 All RLM 02 RLM 02 RLM 02 RLM 02 Planes built after 1941-RLM 66 cockpit
 
C-1 Trader A Dark Gull Grey White White White
 		 Personal experience
EE. Lightning All Black Aluminum Aluminum Aluminum
 
 
F-100 Super Sabre All Black (?) Aluminum Aluminum Aluminum Interior could have been Dark Gull Grey
 
F-102 Delta Dagger All Black (?) Alulminum Aluminum Aluminum Interior could have been Dark Gull Grey
 
F-104 Starfighter All Dark Gull Grey Aluminum Aluminum Aluminum
 
 
F-14 Tomcat All Dark Gull Grey White White White
 
 
F-15 Eagle all variants Dark Gull Grey White White White wheels could be white or silver
 
F-16 Falcon all variants Dark Gull Grey White White White wheels could be white or silver
 
F-18 Hornet all variants Dark Gull Grey White White White
 
 
F-4 Phantom all variants Dark Gull Grey White White White
 
 
F4F Wildcat All Interior Green white white/black lower white Struts that protrude beyond the well - black
 
F4U Corsair -1/-1A/-1D/-4 Interior Green Underside color Underside color Underside color wheels/struts could be aluminum
 
F6F Hellcat -3/-5 Interior Green Underside color Underside color Underside color wheels/struts could be aluminum
 
F-84 E/G Black Yellow chromate Aluminum Yellow chromate
 
 
F-86 all variants Black Aluminum Aluminum Aluminum
 
 
Fw-190A -1/-2/-3 RLM 02 RLM 02 RLM 02 RLM 02
 
 
Fw-190A -4 and later RLM 66 RLM 02 or underside color RLM 02 or underside color RLM 02 or underside color Underside color more likely on late war planes
 
He-111 All RLM 02 RLM 02 RLM 02 RLM 02 Planes built after 1941-RLM 66 cockpit
 
Hunter all variants Black Aluminum Light Aircraft Grey Aluminum
 
 
Hurricane All RAF Interior Green Underside color Aluminum Aluminum
 
 
Ju-52 All RLM 02 N/A Underside color N/A
 
 
P-3 Orion A/B/C EP-3B/E Dark Gull Grey White White White
 		 Personal experience
P-47 Thunderbolt B/C/D Interior Green Yellow chromate Aluminum Yellow chromate
 
 
P-51Mustang D Interior Green Natural metal Aluminum Aluminum Wing spar in well yellow zinc chromate
 
S-3 Viking A/B ES-3A Dark Gull Grey White White White
 		 Personal experience
Spitfire All WWII RAF Interior Green Underside color Aluminum Aluminum
 
 
T-39 Sabreliner E/G Dark Gull Grey White White White
 		 Personal experience
               
NEW ITEMS              
B-52 All versions to 1980 Dark Gull Grey Yellow Chromate Aluminum Yellow Chromate Flap wells and outrigger wells; yellow chromate B-52G Tech Order
B-52 G-H after 1980 Dark Gull Grey ADC Grey White ADC Grey Flap wells and outrigger wells; yellow chromate B-52H Tech Order