If I have a low pass filter, does the choice of window function I use have any effect on the quality of the audio input? What would be the effective difference between using a rectangular window and a blackman window of the same size?
A cursory search of google will give you frequency response plots of various windows, for example: http://www.labbookpages.co.uk/audio/firWindowing.html
By windowing an FIR filter you convolve the frequency response of the filter with the frequency response of the window, as given in the other answer. This tends to smooth the frequency response in a sense, reducing ripples. If you for example require a low-pass filter with fast roll-off, windowing might be counter-productive. On the other hand, if you need flat pass-band, windowing might help. These days windowing is not as useful as it used to be, because when doing FIR filter design using constrained optimization it is usually more straight forward to meet specified performance criteria (but more expensive computationally).