Indeed, a very tough call.
If I'd cut all of it down to some categories:
1) writings or epigraphical items: the Young Indy diary
2) artefacts: something multi-parted that works like a key, like the Mirror of
Dreams which was kinda cool
3) costume parts or apparel: Indy's satchel (because it's practical - unless I was a rancher I could actually use the bullwhip but it just won't be usefull around an office or museum hall)
4) Frankly, I'd be nuts to leave without the miniature model sets (I have a soft spot for): I'd go for the entire desert Tanis excavation set with tent encampments, poles, small rubble-transport rails, storage areas, dig sites, crates, installations and the strip with the Flying Wing...
That or the entire Doom mine tunnel complex with all tracks 'n curves... with actual rolling minecars off course.
I've had this wicked plan of making the Tanis miniature set a long time ago, but I don't have enough schematics nor the time nor the patience to put it all in place...