The Thames Clipper is an absolute gem. There are two sizes - Storm Clipper or much larger Hurricane Clipper, both of which are catamarans, making them speedy and very comfortable.
I treat myself now and get the clipper home from CW to Tower Bridge, it makes a great change from the DLR. You can use a travelcard for a discount. If it was fully integrated into the London Transport system I'd use it all the time.
They aren't terribly frequent, so worth checking the website for the timetable before you set out. www.thamesclippers.com
The clipper is great. I'm staying with my partner at the moment just down river from Greenland Dock and we use it most weekends in and out of town for shopping etc. Unfortunately it doesn't run late enough to get it back after a night out.
My partner uses it to get to work at Holborn Bars (the old Pru building) by going to Blackfriars and then a short walk across fleet street and up Fetter Lane. It is much better than the alternative which involves one bus and three tubes to go about 5 miles, bit dearer though.
Its good - a bit more expensive than the tube (you get a discount if you're a travelcard holder), but worth it in summer. The only trouble is that it doesn't start early enough from London Bridge for a lot of City jobs, stops during the day (would be great to get to meetings by boat) and finishes early. But as a way into the centre of town on a Thursday evening after work, it can't be rivalled IMO - buy your Evening Standard and a bottle of beer and within 30 mins you're at Embankment.