In early September we are staying in Mainz for 3 nights, and Boppard for two nights. We want to possibly visit by train: Bacharach, Baden Baden, Rudesheim, Bingen, Eltville, Oberwesel, St. Goar, Marksburg Castle, possibly Black Forest, Oestrich - Winkel. I know we will never get to all of them. It will be fun just visiting some of these destinations. Which ones should we target and which ones are the best to do geographically from Mainz and Boppard. In other words what would an ideal itinerary be? We arrive in Mainz the morning of 9/3. We would have just flown into Frankfurt and taken a train to Mainz. We will be very jet lagged. We move onto Boppard on 9/6 and take a train back to Frankfurt on the afternoon of 9/8. Thanks for all of your help.
Why are you dividing your time between Mainz and Boppard? They are only 45 to 50 minutes apart by train. It would make more sense to stay in one place instead. Boppard is a good choice - small enough to be charming but big enough to have restaurants and a good choice of hotels (I stayed at the Hotel Bellevue and really liked it).
Also, travel and transferring hotels takes time away from sightseeing. 5 nights really only equals 4 full days, which is not a lot of time.
With 5 nights in Boppard, you could easily see many of the places you list above and do one or more river cruises. For example, I took the train to Bingen, and then a KD river cruise from Bingen back to Boppard (via a transfer in St. Goar), which was incredibly scenic and showed many castles. I would also suggest a trip to Burg Eltz as well as Marksburg Castle.
You really don't have enough time for the Black Forest portion of your itinerary. Just focuson the Rhine/Mosel area - there is so much to see there and with only 4 full days, you will have your hands full just with the Rhine itinerary.
I think the itinerary below gets you to the best spots and is doable. I'm tossing in the town of Cochem as compensation for subtracting the Black Forest from your trip, which is indeed too far, as Mardee points out.
Day 1: I think heading to Mainz first is a wise move. Spend some of Day 1 and some of Day 2 there. But I think that will probably be plenty of time and that one night is enough. I do NOT consider Baden-Baden or the Black Forest good daytrip choices from Mainz.
Day 2: Mainz in the morning and early afternoon. At 14:03 or 15:03, fetch your bags and take the 30-min. train ride to Bingen Rhein Stadt station. Have a meal or some refreshments on the waterfront promenade near the KD boat dock and enjoy the views. Catch the 16:30 "Goethe" paddlewheel steamboat to Boppard (18:50) and you will have seen the best scenery the Rhine has to offer.
Day 3: Combine Bacharach and Oberwesel in one day trip
Day 4: Combine St. Goar and Rüdesheim in one day trip; use the St. Goar ferry (runs every 20 minutes or so) to cross the Rhine so you can catch the train from St.Goarshausen to Rüdesheim.
Day 5: Visit Marksburg in Braubach and Cochem on the Mosel River. Cochem is a lovely town and the train ride along the Mosel River is lovely as well.