Which is the prettiest/coolest town to visit out of these: Linz, Remagen, Unkel, Bad Honnef, Konigswinter, ...

I was thinking of taking the train (or some other means if you have a better idea) to one of the following towns, having lunch & getting a river cruise back to Cologne on a KD cruise (the roundtrips & special itineraries aren't avail on my dates) Which of the following towns would you suggest we eat in & start the cruise from? (Linz, Remagen, Unkel, Bad Honnef, Konigswinter, Bad Godesberg, Bonn, Wesseling)

Ok, if these are your potential starting points to go back to cologne on the KD boat, I would definitely start in Konigswinter, which is just across the rhine from bonn. There is the famous "Drachenfelsbahn" (meaning Dragonmountain train) which you can take up the hill, to go to the beautiful dragon castle.

Here are the links to the train:
http://www.drachenfelsbahn-koenigswinter...

and the castle (german only unfortunately - just press "Rundgang" and you will see some pictures):
http://www.schloss-drachenburg.de/

Re. the train: the train is fine, the direct trains from Cologne main to Konigswinter take only about 35min. from there you can either walk over to the "drachenfelsbahn" or take a cab.

As I live in Cologne and work in Bonn and drive that route every morning so I could also offer you to give you a lift (unless you have a big family as I have fairly small car). Just msg me if you need any other information.

By far the most beautiful part of the Rhine is the one between Bingen and Koblenz. If you want to make a Rhine cruise you should really consider seeing this part as it has the steepest cliffs (including the famous Lorelei rock), nice old villages on both sides and a castle on every other hill. Going only as far as Bonn or the other places around Bonn you mentioned you would miss the best.
There is a daily KD boat that leaves Bingen at 10:30 am and arrives in Cologne at 8 pm. If you make it an early start you could make it easily a day trip. You would have to leave for Bingen by a direct train from Cologne at 7:18 am, which would give you plenty of time in Bingen to get to the wharf, even have a little breakfast or see the Mouse Tower of Bingen. The train goes all the way through the Rhine valley so you can already check what you'll see by boat on the way back.
So think about it!