Well PCI debuted circa 1994 to replace ISA. ISA slots were offered on the majority of mainboards through 2001. PCI Express debuted in 2004 to replace PCI.
Now that so many devices and I/O busses have been moved from the main PCI bus onto the chipset, PCI has been given a new lease on life, in a manner of speaking. Its perfectly adequate for numerous modern devices; video capture and TV tuner boards, sound and DSP cards, 100mb ethernet, USB2.0, Firewire, etc.
Check out the current selection of high-end sound cards at Newegg; PCI v. PCI Express ($50 or higher):
PCI Interface = 20 results
PCI Express interface = 10 results
Similar results for video capture, TV tuner boards, USB and Firewire. Ergo, PCI still accounts for the majority of devices available and should be around for a few more years. You might want to consider USB 2.0 or Firewire, also. There are a number of Pro Audio interfaces that utilize USB 2.0 or Firewire.