Application support for PulseAudio is not quite complete. Notable problem applications are Skype, Flash Player, and Real Player. I shall refrain from my usual sarcastic commentary on the inability of the vendors of closed, proprietary applications to keep pace with FOSS development, because a person should exhibit a bit of class now and then, however insincere. Visit The Perfect Setup for instructions on getting these to work.
I had originally intended to make this as general a guide as possible, but I ran into a number of problems on both Kubuntu Gutsy and Hardy and got all wrapped up in debugging them, so today is going to be Fix *buntu Day. This may be useful to users on other other distributions as well because it covers permission problems, ALSA problems, and init problems, so everyone is welcome to tag along.