PCI latency timers are a method to allow PCI bus-mastering devices to share the PCI bus so that PCI devices won't use such a large portion of the available PCI bus bandwidth that other devices aren't able to get needed work done.
If you have problems with your audio (usually onboard) clicking (while overclocking especially) then setting PCI latency timings to a more mid-range can help set the PCI bus fairly and allow for concurrent requests to be handled in que, giving the audio a better chance to respond to the signal reqeust and hence data delivery.
Hence the audio and other PCI bus issues that can be problematic, and especially so in an overclocked system which can often be attributed to the PCI latency settings.
If the Latency Timer is set too low, then PCI devices will interrupt their transfers unnecessarily often which will effect performance. If it's set too high, devices that require frequent bus access may overflow their buffers and lose data. This is where you will hear crackles in sound and dropped packets in Lan data transfers or web access.
If you are having issues you can set the access (I use 48 clock cycles) and test for issues.