The two bus loops overlap almost completely. What separates them is a stop or two, and where you get on.
Big Bus: the Red route
Ten stops: Louvre-Pyramide (the Big Bus information center at 11 avenue de l’Opéra), Louvre–Pont des Arts, Notre-Dame, Musée d’Orsay, Champs-Élysées, Grand Palais, Trocadéro, Tour Eiffel (Quai Branly, by the north pillar), Champ de Mars and Opéra Garnier. Big Bus says its Trocadéro-area stop has moved to avenue d’Iéna, facing the Shangri-La hotel.
Tootbus: the Blue route
Tootbus is the former Open Tour Paris, renamed by its owner, RATP Dev. Its ten stops are Opéra–Grands Magasins (23 boulevard des Capucines), the Louvre, Notre-Dame, Panthéon–Luxembourg, Musée d’Orsay, Concorde, Champs-Élysées, Trocadéro, the Eiffel Tower and Pont Alexandre III–Invalides. The real differences: Tootbus has Panthéon–Luxembourg and Concorde, while Big Bus has the Grand Palais and the Champ de Mars.
Batobus: the river
Nine stops: Tour Eiffel, Invalides, Musée d’Orsay, Saint-Germain-des-Prés, Notre-Dame, Jardin des Plantes, Hôtel de Ville, the Louvre and Place de la Concorde, about 15 minutes apart. The boats are glass-covered, heated and seat 180, with an open-air deck. There are no toilets on board. Large bags and suitcases are not allowed through the boarding security check.
The Batobus is a shuttle with a view, not a commentary cruise. For a one-hour cruise with live or recorded commentary, see Bateaux Mouches vs Bateaux Parisiens. If the Eiffel Tower is on your list, book the summit separately: Eiffel Tower tickets explains the options.