I see that a lot ICs for PC use a single 14.318 MHz crystal oscillator (which is an NTSC standard frequency, so very widely available in terms of parts) to generate the clocks for PCI, USB, etc. Here's a table from one such chip, ICS932S421B.
How does this work? These don't seem obvious multiples.
I found an older datasheet RTM520-39 that at least has clue for the 33.33 MHz (but not for 48.000 MHz): 149/16 * 14.318 = 133.34, which divided by 4 gives a decent 33.3341 MHz PCI clock. For USB it said that it used 107/16 * 14.318 = 95.75 MHz and then divided by 2.
Also worth noting here is that more recent PC ICs, e.g. SLG84901, use a 25 MHz reference clock, which surely makes PCI Express (100 MHz) clock generation simpler.