If you want to see Paris from the Seine, there are several companies available (I'm think of the Bateaux Parisiens, Vedettes Pont-Neuf and Bateaux Mouches). However, if you want to travel rather than sightsee, things get a little complicated.

The Batobus service which has eight stops along the central portion of the Seine is not really a bus at all, is horribly overpriced (12 euros for a one-day pass!) and not very frequent. So what do you do if you've booked a hotel in, say, exotic Maisons-Alfort rather than one of our lovely establishments in the centre of town? The latest answer could be Voguéo.
Hotel Paris
photo (c) STIF

A test service has just started, running up from the eastern suburbs to the Gare d'Austerlitz. It's free for anyone who has a weekly or monthly travel pass (3 euros for anyone else) and there's a boat ever 20 minutes or so starting from 7am in the morning and finishing around 8.30pm.
Hotel Paris
It'll run for a couple of years before a decision is made to extend the service (or not) further into town, or to run a similar system for the west of the city. For those coming into the city from the east, it could make the journey more agreeable. Some people are already saying that it gives them the impression of being on holiday every day! Let's wait and see what they say when it starts getting cold and rainy... ;-)

More info on Voguéo (in French, darnit) here. You can download a PDF file of the timetable here.