For making keying interfaces you can buy transistors with the pull up
resistors built in 
My personal favorites come in SMT format and are small enough to easily
build into pretty much any connector 
you can read more here
http://www.fairchildsemi.com/products/transistors/integrated_digital_transistors.html
these are seriously useful devices for all sorts of hackery.


My 'vote' is in favor of having general purpose I/O pins and doing the
interfacing externally. 

73's  
brendan EI6IZ (waiting impatiently for my K3 :-) 

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