Flexible PWM including phase control of multiple channels

That is starting to look a bit like a serial data stream and if your modulation patterns are simple enough, perhaps you could achieve them as a bitstream.

Failing that, I remember reading about an Arduino tone generator project which worked on the basis of a timer triggering at a frequency which was suitable higher than the frequencies of all the tones that needed to be generated and just toggled the outputs high and low at the appropriate times. I'm sure that Googling for Arduino tone generator would find it for you.