My favorite model is easily Bill Cunningham's "Grand Sport Corvair" that was in Scale Auto Enthusiast. He did this stellar GT40-style clamshell rear deck and dropped in a hyper-detailed version of the Accurate Miniatures Corvette Grand Sport's small block Chevy, complete with quad side-draft Weber intake. The interior was practically all scratchbuilt and he did all the photetch himself. He even custom machined the wheels from round stock aluminum and scratchbuilt a nickel plated front bellypan.
The whole car was painted in a gorgeous Pearl White. One of my long LONG running projects is to replicate the build, but I'm using a big-block from an Accurate Miniatures McLaren M8B and am adding candy blue pinstripes.
I've only got as far as cutting up the chassis plate (on a $30 Prestige series issue of the AMT 1969 Corvair
).
Runner up, though I can't remember exactly who built it at the moment, is this 1/8th scale entirely scratchbuilt model of Mike Muldoon's #50 Oswego Supermodified that was at the Toledo NNL. It was incredible, plus I'm a huge Supermodified fan.