A curious tension exists in Geneva between dour intellectual concepts and breathtaking physical beauty, and you will probably find yourself torn between the urge to wander the quays and the sense that you ought to hit the museum trail. Don't choose: try to divide whatever time you have in the city equally between an extended stroll along the waterfront and a thorough exploration of the Vieille Ville.
Make time for the International Area if it interests you—never mind if it doesn't. Do not, however, skip Carouge, the creative, convivial warren of craftspeople and artists to the south of the city. Do try to see some specialist collections (the Fondation Bodmer and the Patek Philippe Museum are stars), do check out the Rues-Basses shopping scene, and make sure that you go somewhere—Port Noir, the tip of the Jet d'Eau jetty, the cathedral towers, La Perle du Lac, Cologny—where you can see distance: Geneva genuinely does look equally good from up close and far away.
With that in mind, here's a sample itinerary that hits all the bases in three days. Spend your first morning exploring the downtown waterfront, with its boats, swans, 15-foot-wide flowered clock face, and feathery Jet d'Eau.
Then window-shop your way along the Rues-Basses and up into the Vieille Ville. Have lunch on place du Bourg-de-Four, and investigate the Espace St-Pierre, an umbrella term for the starkly beautiful Cathédrale St-Pierre, Musée International de la Réforme, and underground site archéologique. Don't forget the contemplative Auditoire de Calvin (if it's open); the Monument de la Réformation sums it all up.
The next day head for the International Area. Spend the morning at the Palais des Nations and the Musée International de la Croix-Rouge, have lunch at the Château de Penthes, and spend the afternoon wandering the Jardin Botanique. Then head over to Carouge for a late-afternoon stroll through galleries and craftshops.
On your third morning, head back to the Vieille Ville and work steadily through the Maison Tavel, Musée Barbier-Mueller, and Musée Rath. Eat lunch near Place Neuve, and then explore watchmaking at the Patek Philippe Museum, watch history unfold at the Fondation Bodmer, or take a break and spend the afternoon riding the waves of Lac Léman on a Compagnie Générale de Navigation (CGN) paddle steamer.