Basel.
The only advantage of starting there is you can say that you have cycled all the way from Switzerland.
Basel is the industrial capital of Switzerland, no chocolate, no cukoo clocks.
Mulhouse.
Marginally better
However I seem to remember the stretch between Mulhouse and Strasbourg is pretty flat and boring
Strasbourg.
May well be the best place to start,
It about 500 bike miles/10-15 days to Amsterdam, 100 miles/2-3 days more if you start in Basel.
So really it is down to time. If you only have two weeks then start in Strasbourg, if you have 3 then start in Basel
Another option worth looking at is to start on the river Main, it joins the Rhein at Mainz
I'd also strongly suggest you buy the Bikeline books on cycling on the German rivers. The maps are superb (all the text is in German, but if, like me you don't speak a word you can still work out were all the camp sites etc are )
Work on where you need to be at the end and then count the days back from there assuming about 50 miles a day. The advantage of the Main/Rhein is you are never more than 5 miles from the railway line, so if you get to a boring bit, or you are running behind time, or it's raining, you just hop on a train for a few stops
