The Rhine from Koblenz to Mainz

I wouldn't do the whole area by boat, just the best bit in the gorge, and it would take one day or less. The west side has traditionally better train and boat service, with more interesting towns. Good stuff on the east side, too.

There are hourly/bi-hourly regional trains on both rail lines (there is one each bank of the river). It takes 1h30 to travel there. As for "how much time to spend", it really depends how much you want to visit and what activities you want to do. I recommend going to the Loreley rock. You can also visit the sister villages of St. Goar and St. Goarhausen. I'd not be so fixated in travelling the whole stretch by BOTH train and boat.

What side of the river would be the best to hop-on/hop-off the train. Are there more to see and do on one side opposed to the other?

If you look at a Google map of the Rhine, you can see which towns are on which side. On the right side, the towns that I would recommend would be Elteville, Rüdesheim, Lorch, Kaub, and Braubach. Rüdesheim has the wine museum, and the chair lift up to the Niederwald Monument. It can be very touristy, though lots of people enjoy seeing the town itself. Near Elteville, a town that no one seems to talk about much on here, is the Eberhard Monastery where the Name of the Rose was filmed. Very impressive place. Lorch has one of the most stunning medieval, carved, wooden altars along the Rhine, and is 14 meters tall. Braubach has the Marksburg Castle. Kaub has Pfalz Grafenstein, a castle built in the middle of the Rhine. The Loreley is the biggest let down. Just a tall cliff, and a very small statue sitting on a spit of land extending into the river. Not something I would go out of my way to go see, especially on a short vacation. The Left hand side of the Rhine, has Bacharach, St. Goar, Ober-Wesel, and Trechtingshausen. All have interesting churches or castles to visit. My tip is more towards visiting the towns on the left hand side. Perhaps get on the boat at Rüdesheim, and take it all the way up to Braubach, tour the Marksburg, take the ferry across to the other river bank and continue south along the Rhine, by train.

If you want to really see the area I think 3 days is about right. Pick a town on the west bank ("left" side) and stay in one place, then do outings. St. Goar is great for this purpose, but Boppard or Oberwesel will work too. The cruise is nice if the weather cooperates. It can be done as Jo suggests - start in Rüdesheim (or across the river in Bingen) and cruise north, and stay on the boat, as a matter of priniciple, since the boat schedule makes hopping on and off somewhat inconvenient. The cruise to Braubach (nice town, Marksburg Castle is great) takes 3 hours; getting up to the castle, taking a tour, and having a little refreshment at the castle terrace-cafe will take 2+ hours. (Don't cruise from Braubach to Koblenz - the scenery isn't all that, and the Koblenz dock is a long way from the train station.) Doing it this way requires the better part of a day and an early start - there is no boat from R'heim to Braubach after 10:15 and before 14:15, and the 14:15 boat arrives quite late (17:20) in Braubach. As far as I know, there's no ferry from Braubach - maybe Jo can clarify - but you can take the train back to St. Goarshausen, then ferry over to St. Goar. The cruise is nice as an introduction to the river. If you arrive in the area in R'heim or Bingen around noon or later and want a cruise, then cruise a little less of the river - get off in Boppard, or maybe before that St. Goar, depending on where you're staying. You can take your bags on the boat.

(cont.) Let's say on Day 1 you arrive by train in Bingen at 2:00 pm. Catch the 14:30 boat to St. Goar (15:55) and drop bags at hotel. What then? I'd visit Bacharach by train (10 minutes) and plan on a meal there, then return to St. Goar whenever. Then on Days 2-3 you can do daytrips. One day for the east bank - visit Marksburg (ferry across from St. Goar, runs all day; then a 20-min. train ride from St. Goarshausen to Braubach.) After Marksburg train to Rüdesheim and maybe Kaub - then return to St. Goarshausen and ferry over to St. Goar. Another day for the west bank - train to Oberwesel (5 min.) and Boppard (10 min.) and of course St. Goar itself (Rheinfels Castle.) If you have more time or can squeeze it in as you come or go, Linz (north of Koblenz on the east bank) is maybe the most attractive town in the whole area. Your daytrips on days 2-3 or 2-4 can be done by regional daypass - the Rheinland-Pfalz ticket costs 26€/day for two: R-P TICKET

Thank you for all the great Information. I really helps with planning.