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Not necessarily

Your advice of keeping the PCI bus relatively "free" to avoid contention with the sound card is good. By the way, the goal is not necessarily to have "ultra low latency playback" - it's to have low jitter. In fact, typical solutions to reduce jitter often increases latency (ie., memory buffering). Fortunately, latency is not a problem when you are just listening to music (it is however an issue if you are watching video at the same time).

However, depending on the motherboard chipset, USB may or may not go through the PCI bus. For example, on newer chipsets, USB support may be handled through a PCI Express bridge rather than PCI.

Also you don't need to use USB devices for flash. For example, you can use a compact flash card and a a CF to IDE bridge and connect it directly to your IDE port.

A good soundcard should have some internal buffering and also act as a PCI bus master. So hopefully it should not be impacted by other PCI devices (provided it gets allocated a dedicated PCI interrupt line). Generally, the only device that tend to cause problems for PCI sound cards is graphics cards that hog the PCI bus (by having excessively high PCI bus latency). Fortunately, this should no longer be a problem with PCI Express x16 cards. Also, motherboard Gigabit Ethernet chipsets tend to bypass PCI as well.

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