One reason I don't use the klong boats is you get dirty water sprayed in your face. A route of interest to me is the one along Saen Saeb towards the river but I believe you have to change boats before you get to Rattanakosin Island.
Not that long ago I took a river ferry in Bangkok for the first time. They're a great way to get around, with the limitation that they only travel along the river. One trip of any distance costs 15 baht, and affords a different look at Bangkok, the usual mix of old and new buildings but from a different angle. My wife was afraid to use it because apparently one crashed a decade or two ago but once she gave in my kids loved it. I ran across a general transportation reference site as well, which goes through BTS, MRT, airport link, those Express ferries, even khlong boats. It just stops short of explaining how to use local trains, which probably wouldn't make sense for most anyway. The site has a route finder that can identify which buses go from one place to another, but it only covers a limited set of points. http://transitbangkok.com/