For what it's worth, here's what I gleaned from my journal of our 2010 Rhine and Mosel cruise:
In Antwerp we did not tour the 15th Century Cathedral of Our Lady, but the tour guide talked a lot about it as we viewed the exterior. The tour ended in the square in front of the Cathedral so that those who so desired could attend the 12:00 Noon mass.
In Nijmegan we also saw the outside of the cathedral while our PD talked about its history and pointed out the "Devil on a pole" in front of the cathedral.
In Bonn we saw the Jewish enclave as well as the Church of St. Martin. Neither was specifically toured but both were discussed by the PD. On an optional tour we went to Bruhl and toured Agustusburg Palace, the very opulent residence of the Archbishop of Cologne, but it had little religeous significance.
In Trier we viewed the oldest cathedral in Germany and had a very detailed discussion by the local guide, but we did not enter it.
If we saw a cathedral in Luxembourg it did not impress me enough for me to remember it. But the prayer chapel at the American Military Cemetery, and the whole cemetery itself, was a spiritual high for me.
As we walked into Speyer from the ship the cathedral and its surroundings were pointed out and discussed, but our tour of the cathedral was done on our own time and by our own designs.
The Cathedral in Strasbourg was about the most spectacular I have observed. Our PD led us around and then into the cathedral for a guided tour.
In Basil we toured, inside and out, the cathedral, once Catholic but now Lutheran.
In Lucerne (post cruise exension) we toured rather intensely the Jesuit Church of Lucerne as part of the included city tour. Although it is still an active church it is more frequently thought of as a concert hall and tourist spot. It is somewhat unique because of the combination of Baroque and Rococco style.