Church of Fause, downstairs-Periodically a character will show up and award your players with a boost. So far I've come across a slime, and a robot. Might be worth checking this basement out each time you complete and return from an area.
Statue of the Hero, Faust-Visit the statue each time you complete and return from an area for a potential boost. (@kimo)
Visit the Temple of the Void each time you return to Faust with a recruited god/goddess to spawn another Eye of the Void. You can get at least 3 more after the original.
Metal Fortress-Basement, Level -1, accessed by the stairs in the left lower corner of Level 1- Just above the raised area with a switch are 4 statues. There are 3 braziers to the side of 3 of these statues. One statue is missing a brazier. Walk up the side of that statue where the brazier should be and your party members will instantly be blessed with +1 Level. It might be worth waiting until you have Kraken in your party before doing so, as you'll probably be returning here anyway to gain the boosts of the 2 boulders in this area.
Metal Fortress, Level 2-Follow the signs and walk the path. Just sayin'.....
Unfortunately, it seems to be only a temporary boost.
Metal Fortress - There is a set of stairs leading to the basement (lv-1) that's not mentioned in the guide. Lots of goodies there (@kimo) and also a portal the the witch's house (@Lis) [Reach this area from the stairs in the upper area of level 1 just after you cross from the left map to the right map. Make sure you have the Orb of Truth equipped or you won't be able to see the portal. Be sure to grab the Gabura doll from the table.]
Metal Fortress-Throne Power Room-return and inspect throne once to find gold, second to find an azure pearl.
Crock'pond-Return to Crock'pond and visit the harpy after defeating the mushrooms and she'll reward Luke with +1 AGI and a skill boost.
Drone-In the NE building there is a piano downstairs and a despondent man directly above on the main floor. He mostly is annoyed with the music coming from the piano below, but there is one tune that will make him cheerful, at least for the moment, and he'll gift you a Mutical Box.
Zarmazari Breach - Again, you need to have the Orb of Truth equipped to see the portal
kimo wrote:There is a Witche House entry that appears in the Breach. It appears as a glowing arched portal in the north wall of the map just before the final map with all those dark chasms.
Cosmic Plane-There are invisible paths to chests, looks like all are attainable, none are teasers.
The Core-Metal pliers -looking for how/why it's used. Indy says it has a definite use
Kranko-Periodically Kranko appears, seeking to destroy Luke and his party. Indy says there's a definite significance to this character. Looking for more info.
Don't tell Indy...
Aldorlean Ladies! 
