Wow, the Lapin Agile is a real place? I'll have to go there on my next visit!
Some suggestions for you & your girlfriend:
Army Museum (Musée de l'Armée)
, 129 Rue de Grenelle, Esplanade des Invalides
A wing of the museum is dedicated to WW1 & WW2. (This is my favourite war museum...for the immense collection of Napoleonic stuff.)
Place de la Concorde
Where Indy played on the fountain in "Paris/Passion for Life". It also has the Luxor Obelisk from Egypt which can be seen in the same shot. (This is across the river from the Army Museum so you can pass by on your way there.)
Alexander III Bridge (Pont Alexandre III)
Indy & Miss Seymour walked across this bridge. (This is the next bridge west of Place de la Concorde and leads directly into the esplanade of the Army Museum.)
For the Indiana Jones rollercoaster, Le Temple du Péril.
Sorbonne (University of Paris)
, 1 Rue Victor Cousin
Where Indy studied in the Bantam novels.
Guimet Museum (Musée Guimet)
, 6 Place d'Iéna
Where the real Mata Hari performed her first dancing shows. The museum's founder was also one of her lovers. Inside is a large collection of archaeological sculptures & art from the Far East.
Élysée Palace Hotel
, 103-111 Avenue des Champs-Élysées
Where the real Mata Hari was arrested in her hotel room. (Not to be confused with the proper Élysées Palace where the French president lives!)
Cinema Museum (Cinémathèque Française)
, 51 Rue de Bercy
Not necessarily Indy-related but interesting, nonetheless. It has a insane costume designed by Picasso which is very similar to the one his girlfriend wore in the "Barcelona/Espionage Escapades" episode. I thought the costume was dreamed up for the TV show but, apparently, it wasn't.
, 1 Avenue du Colonel Henri Rol-Tanguy
A huge, creepy underground maze filled with human skulls & bones!