Are there any remote/receiver products out there that fit this description?

I have an open 3.5" drive bay on the front of the case I'd like to use for my HTPC. Rather than buy an external IR receiver that plugs into a serial or USB port and sits next to the HTPC case, I'd like a receiver that just occupies the 3.5" bay and connects via an internal cable to a serial or USB header on the motherboard.

IOW, I want to add a remote to a computer without any external bits laying around outside the case ... and I've got a convenient 3.5" hole in the front of it. Thanks.

If your MB has either a serial or usb internal connector, just use it inside the case and mount the actual receiver in a blank 3.5" cover. Should be a fairly simple matter.

iMON makes exactly what you want:
iMON VFD (http://www.soundgraph.com/Eng_/Products/imon25.aspx?topMenu=2&subMenu=1&leftMenu=25)
iMON Inside (http://www.soundgraph.com/Eng_/Products/imon24.aspx?topMenu=2&subMenu=1&leftMenu=24)
(Except that it fits the 5.25" bays)

You can purchase it from pcAlchemy:
http://www.pcalchemy.com/index.php/manufacturers_id/57

I don't know about Linux support. A version is included in the popular Silverstone and Ahanix HTPC cases, so I think some Linux support is available.

I also have a case that has a rack to internally mount a Windows MCE remote. You have to remove the plastic case to mount it. If you're handy, you could do that to a 3.5" bay.

Lirc supports IMON in several forms. http://www.lirc.org/html/table.html

there is also a nice configuration website http://lircconfig.commandir.com/ to help you with tweaking your remote bindings.