Hi Shawn,
 
Thank you for your quick response. 
• Please submit any development bugs as a Ticket [1] 
Yes I will, as soon as I'm sure that it is not me that is the cause....
 
• Everything must be compiled 64-bit for Snow Leopard (10.6.x) 
I did. But strangely, running a "file" on ifd-ccid.bundle/Content/MacOS/libccid.dylib tells me that it's only compiled for 32 bit (i386 and ppc)
 
• ifd-ccid is actually statically linked to libusb and not IOKit 
Okey, I see that now. /usr/local/bin/libusb-config --libs gets me libusb too. Sorry my misstake.
 
• You can not just build your *own* version of pcsc-lite 1.5.5 (pcscd) for Mac OS X, since there 
is a fair amount of Apple addtional code to integrate with securityd.  The v1.4.x that is included
in Mac OS X is posted under the Source Branch. 
I was actually trying to de-integrate them by renaming pcscd to pcscd.new and run that from the shell with the additional --debug option. It's a bit strange that the arguments of pcscd are hardcoded into securityd and there 
is no way (that I saw) to pass additional arguments.
 
B.t.w. If I boot the Mac with a reader connected and with a standard cell phone UICC inserted (containing no login token or anything) it seems like the login
window just flashes between the normal login screen and an all-blue screen, and you're not able to enter your password as during a normal (username/password-based) login.
I had to move the "builtin:smartcard-sniffer" down below the "builtin:authenticate,privileged" entry under "system.login.console" key in the /etc/authorization file. (also moved it under the key "authenticate").
This happens with the orignal versions of pcscd and ifd-ccid, so it's not something I indueced. This issue might be "off-topic" but you might be able to direct me to the appropriate place.

Is it possible you are using Extended APDUs ?  Note at the Smart Card Reader Matrix [2] for the CCID Reader Driver that for the 3121, supports "short APDU mode" [3].
I  am using short APDUs. My standard test APDU  is "00 a4 00 04 02 3f 00" (select master file and return FCP)
 
Regards
/Patrik