I believe most of the types of products you're looking for don't interface to the PCI bus directly. Instead, they convert the SD or CF card to IDE/PATA or SATA, connecting your flash card to an ATA controller. (I expect this is what the Chumby does for its "internal 2GB microSD card", though I can't find direct confirmation of that.)
For example, this Addonics cardreader reads SD/MS/MMC cards, provides a a standard 40-pin IDE connector. You can connect this to a motherboard or PCI IDE controller, and is available mounted in a 3.5" drive bay bracket or in a PCI bracket, like this (note it's not plugged into the PCI slot, it's just mounted in the space above it):
These products are something of a niche, but there are many options in that niche. Most products seem to be designed for CF rather than SD; I've seen several CF-to-SATA adapters but no SD-to-SATA adapters. You could chain the SD-to-IDE adapter above to a IDE to SATA adapter to connect to an SATA controller instead of an IDE controller. I personally distrust this type of adapter chaining, but if a straight SD-to-SATA adapter isn't available it might do.
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