Ubuntu looked awesome and mostly things worked.  But in the months since I pretty much stopped using it, I found that a different distribution is doing more work to help out on the smart card front.  I switched to Fedora Core 6. 
 
The primary motivation is that my smart card compiled library stopped working everywhere and the new recommendation was to use CoolKey from fedora.  I suffered through a pile of I-don't-what-version-it-is problems and finally got to the point of having the library detect the smart card.  Nothing I did made the smart card actually work with Firefox again.  Then I was tempted by the smart card login idea.  I never got that work either.  The last straw for Ubuntu was installing the Lotus SameTime 7.5 client.  It was an RPM and it refused to install because of missing dependencies.  I couldn't figure out why, although the dependencies were there, it wouldn't install.  ...then the Ubuntu color of yellow/brown/orange started getting to me.  
I installed FC6 and appreciated the blue-ness.  CoolKey worked out of the box.  All I did was install the Firefox plug in for DOD.  Its a huge time saver.  Also, I think I may have had to install the CoolKey security device myself, but that was easy.  Magic, and then the smart card worked.  Then I tackled the smart card login.  Everything was already installed for it as well, except for the Root certificate authority certificates.  I needed to install the ones that correlated to the smart card I was using.  Then I just followed the instructions that I'll have to post here later since I can't remember them.  Then it just worked with the USB reader.
 
 
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