What is the best train to take from Munich to Basel?
Given the delay-prone track works situation in the Mannheim / Frankfurt region, I would not take the route via Mannheim, but the one via Lindau and Zurich. Search the DB website referenced above for connections with a stopover in Zurich. If you book early you can get tickets from € 29.90 ("Super Sparpreis Europa", but non-refundable)