Here is your detailed scene-by-scene guide to the film locations in the first Indiana Jones film! I realize it's incomplete in many places, but I've provided all of the clues I've been able to come up with. Everything is plotted in the Google Map below.
The "Paramount" mountain was Anahola Mountain in Kauai (thanks to jones junior).
The jungle travel shots (with stand-ins for the actors) were shot in remote areas of Kauai using a 2nd unit crew.
The spot where Indy & his guides take a break (and one pulls a gun on him) was at Kipu Falls, Kauai. This spot is a popular tourist attraction & swimming hole.
The Peruvian temple interior was built entirely in soundstages at EMI Elstree Studios, England.
The entrance to the temple was a facade built by the film crew on the shore opposite Kipu Falls on Kauai.
The escape from the jungle was filmed on private property on Kauai, possibly off Aliomanu Road, facing west.
Indy's swing & jump into the water and getaway on Jock's plane were filmed on a rice ranch on Huleia Stream, not far from Kipu Falls. Kipu Ranch Adventures offers tours of this location (even allowing you to re-create the swing) as well as other movie locations in the area.
Jock's actual plane from the film is on display near the Temple of the Crystal Skull ride at Disneyland Tokyo.
The exterior of Barnett College was the Faye Spanos Concert Hall of the University of the Pacific in Stockton, CA. It is located at 3601 Pacific Circle. The exact same shot was re-used for Kingdom of the Crystal Skull.
The interior school scenes were filmed in Rickmansworth Masonic School in England.
The lecture hall scene takes place in the Great Hall of Ricksmanworth Masonic School.
Indy's house exterior was was filmed at 38 Alder Drive in San Anselmo, CA (thanks to VP).
The interior of the house was built as a set at Elstree Studios.
The Pan Am Clipper float plane was actually a Short Solent flying boat. The crew found one on land in renovation in the Richmond marina near San Francisco. They shot Harrison Ford entering the plane here, and composited it with a matte painting to make it appear the plane was in water. The same plane is now on display at the Oakland Aviation Museum in California, and you can even go inside it.
The only exterior shot of "The Raven" bar was a matte painting.
The interior of the bar was filmed on Stage 2 of Elstree Studios.
The rooftop of Sallah's house was shot somewhere in Kairouan, Tunisia.
The Cairo street scenes were filmed throughout Kairouan, Tunisia.
The market square where Indy shoots the swordsman (and later returns the truck) was filmed on Pl. Zarrouk, near the Three Doors Mosque in Kairouan.
Iman's house was realized as a set at Elstree Studios.
The Tanis dig site was an enormous outdoor set built on location in an area known as Sedada, near Tozeur, Tunisia.
The inside of the map room was built on Stage 5 at Elstree Studios.
The interior of Marion's tent was filmed on Stage 1 of Elstree Studios. This may have just been the night scene with Belloq.
The nighttime scene above the "Well of Souls" was a set built at Elstree, with the background projected behind the actors.
The "Well of Souls" was constructed as a gigantic full-size set inside Stage 3 at Estree Studios.
The Flying Wing was built at Elstree Studios & shipped to Tunisia, where it was reconstructed on an airfield set near the Tanis dig site in Sedada, near Tozeur, Tunisia. It was destroyed for filming. The pad that it sat on was actually made of concrete, and remnants of it still exist at the location.
The truck chase was filmed at multiple different areas in Tunisia. I'm not sure exactly which shots were at which locations. Portions were filmed near the Tanis dig site. 2nd unit crews shot much of the action on "Paradise Road," near Metlaoui, Tunisia. Where exactly that road is, I'm not sure. Judging by aerial views, that whole area is a maze of windy dirt roads, so any accurate guess could only be done by actually going there.
The close-ups of Harrison Ford being dragged behind the truck (and possibly the other shots in this portion of the scene) were filmed near a phosphate works near Metlaoui. In the background of this shot, you can even see a conveyor belt (blurry in the photo) which is likely part of this operation.
"Omar's Square" was filmed on Pl. Zarrouk, near the Three Doors Mosque in Kairouan.
(See attachment below)