While not Indiana Jones specific per se it does answer that longstanding question of 'What if Tom Selleck Had Played Indiana Jones?' (and was dubbed over by Patrick Warburton.) Introducing the legendary... Reno Jackson!
He's the leader(?) of Blizzard's League of Explorers!
And we are indeed are explorers! Adventure we seek 'cross land and sea!
In the second episode of Gravity Falls' first season, Dipper is imagining the press tour he'll go on after he wins the monster photography grand prize. As he's being feted as a fearless adventurer, something suspiciously similar to the Raiders March plays in the background.
Given the type of show I wouldn't be surprised to see several other references as time goes by.
Deborah Landis and Random Guy on the Internet get into a brief spat over the origins of Indiana Jones' costume. He says Greatest Show on Earth. She says Secret of the Incas. The internet is briefly amused.