3 day Dec. tour, based in Mainz

Since you will be traveling almost entirely in Rheinland-Pfalz, you can both travel all day on the regional trains for 27 euro after 9 am weekdays with a single laender ticket. So you could go to Cochem and back with a stop off or two no problem. You could go up one side of the river and down the other. There is a railway bridge in Koblenz. Now the east bank of the Rhine is in the state of Hesse south of Kaub, so you would need to supplement your laender ticket in that section. You could start your day early on that side with a point to point ticket to Kaub and time it so you got there after 9 am when the laender ticket kicks in.
The ferry at St Goar-St Goarshausen operates every day.

Don't miss the sights in Mainz - the Chagall stained glass, the Roman ruins, the Gutenberg Museum and the Dom.

Be sure to check opening days before you plan any activities. Burg Rheinfels was closed when we were there in Dec. 2011

"Now the east bank of the Rhine is in the state of Hesse south of Kaub, so you would need to supplement your laender ticket in that section."

Actually, the Rheinland-Pfalz-Ticket is valid for travel on the right bank of the Rhein from Wiesbaden to St. Goarshausen on the line including Rüdesheim and Kaub (see map).

It's also valid for the rail line between Mainz and Wiesbaden, to Bonn, Mannheim, Karlsruhe, and more, and on the rail line on the right bank of the Rhein between Karlsruhe and Mannheim. It's even valid to a couple of towns in France (Elsass).

If you'd like to stay around Mainz, Mainz itself has a Christmas Market. Also in the area are Wiesbaden across the river--they have a market http://karilogue.com/wiesbaden-lights-wine-christmas/ and, just up the Rhein, Rüdesheim with its market- http://karilogue.com/lights-coffee-ponies-at-the-rudesheim-am-rhein-christmas-market-of-nations/ . I agree with the user who suggested a visit to the Gutenberg Museum, as well, if you're interested in history, printed materials, or seeing an original Gutenberg Bible.

Just now seeing your question about Rheinfels. It's a favorite of mine because of the tunnels - http://karilogue.com/the-tunnels-nooks-and-crannies-of-burg-rheinfels/ but if you want a castle that's more intact, beautiful, and won't have you bending over in the dark, Burg Eltz is a little bit up the river from there - http://karilogue.com/burg-eltz-medieval-beauty-that-has-stayed-in-one-family-for-33-generations/ I would recommend either of them, each for their own reasons.

I really enjoyed the Christmas markets of Mainz and Wiesbaden. Of all the markets I visited (about a dozen towns), Frankfurt seemed the least attractive, most commercial. There are lots of interesting places for sightseeing, though.

jovitajim.evergreen: Go with kariann.marti's suggestions for the Rüdesheim and Mainz Christmas markets - IME really good ones in their own unique ways. Her suggestion for Burg Eltz is also sound - a great castle - but it's closed after Nov. 2.

Rheinfels is also out of the question. It's closed after November 10.

Marksburg in Braubach is easier to reach than Eltz; it's also a never-destroyed, intact castle with a very good tour. And it's open daily from 11 to 4 (except on Dec. 24 and 25 of course.) If the weather is bad or you're not up for the 20-min. uphill hike it takes to reach the castle, see about getting a taxi.

Marksburg website

":.. is ferry travel across river limited in winter?"
The St. Goar - St. Goarshausen ferry runs all day long and leaves town every 20 minutes or so. It's convenient for switching river banks if you're using the trains. You could visit Bacharach, Oberwesel, and/or St. Goar on the left bank, cross to the right bank on the ferry to St. Goarshausen, take a train 20 min. north to Braubach for Marksburg Castle, then return south along the right bank to Rüdesheim for the evening (the best time to see R'heim's market, IMO.)

It is also possible to reach Braubach from the left bank by traveling by train via the left bank towns to Koblenz (30 min.), laying over there for a while, then catching another train to Braubach (10 min.) This route would allow you a stop in the attractive left-bank town of Boppard as well, but it will probably take longer if you're only going to Braubach.

I think you will find the above towns more than enough for a one-day outing. Cochem is very nice but probably wouldn't add enough to justify the extra travel at this time of year.

I would suggest the Rheinland-Pfalz ticket (daypass, €27 for two) as the best option for the above outing. The pass is good on the St. Goar ferry as well. There's an after-9 am restriction on the use of this pass. But if you do this outing on a Sat or Sun there's no restriction and you can leave earlier than 9 am (which will help you maximize your daylight sightseeing hours.)
Rheinland-Pfalz ticket

There is also a ferry across the river at Boppard, but the landing on the other side is about a km walk from the closest station in Filsen, from which it is a short (7 min) train ride to Braubach.