I can't offer any advice for France, but for the other countries:
Switzerland: My favourite part is the Graubünden. It's certainly the wildest and most remote. However most of the mountainous parts have some good cycling, just try to avoid the traffic (Swiss drivers can be intimidating).
Italy: I'm guessing you are going to stay in the north, in that case the Dolomites are a must. Definitely the most scenic part of the Alps. The Italian lakes are worth a visit too, Lake Como a personal favourite. If you are heading out of the mountains then Verona is an obvious destination.
Austria: Leaving the Dolomites the obvious route across Austria would be the Grossglocknerhochstrasse - and a destination on itself for the sheer awesomeness of the climbing. It's supposed to be easier from the south. However it may still be closed in May and you might have to find an alternative. The Brenner is the obvious one but it is boring.
Germany: The best parts of Germany are the small towns, and in Bavaria you can't go wrong. Assuming you enter Bavaria at Kufstein or Salzburg, I'd go something like Landshut - Ingolstadt - Nordlingen - Rothenburg. If you take the Brenner I'd enter Germany at Fussen, then Garmisch-Partenkirchen and north to join this route. But you can't take a bad route through Bavaria.
From Rothenburg I'd cross the Rhine at Worms then cut across to Bingen. The best part of the Rhine is between Bingen and Koblenz, so you could follow this, or cut across to the Mosel which is even nicer.
Low Countries: From there I'd probably cut across northern Luxemburg into the Ardennes, say to Huy.
Then it depends where you want to finish. If you are heading to the Netherlands probably the most interesting route would be to head across Flanders, Brugge is the classic Flemish town but Gent, Mechelen and Geraardsbergen are all worth visiting (and climb the Muur if you go to Geraardsbergen). Then head north across Zeeland towards Rotterdam.
There's quite a few ideas there. My final advice would be to be flexible: don't follow any route too rigorously and be prepared to follow any road which looks interesting.
