The majority of fast millisecond pulsars are in binary systems, so that any periodic signal they emit is modulated by both Doppler and relativistic effects. Here we show how well-established binary models can be used to account for these effects in searches for gravitational waves from known pulsars within binary systems. A separate issue affecting certain pulsar signals is that of timing noise, and we show how this, with particular reference to the Crab pulsar, can be compensated for by using regularly updated timing ephemerides.