Packages with the pci use flag

app-emulation / vice : The Versatile Commodore Emulator

Enable PCI device discovery using sys-apps/pciutils

app-misc / ddccontrol : Control monitor parameters, like brightness, contrast, RGB color levels via DDC

enable direct PCI memory access (the setuid ddcpci util)

net-analyzer / net-snmp : Software for generating and retrieving SNMP data

Use libpci (from sys-apps/pciutils) to look up network interface description. This feature is only available on Linux.

sys-apps / hwloc : Displays the hardware topology in convenient formats

Enable PCI device discovery using libpci

sys-apps / superiotool : util to detect Super I/O chips and functionality

Support for PCI-attached "Super I/Os" (e.g. in VIA VT82686A/B).