I certainly try to mimic the markings on the actual device and have them visible once the component is mounted to aid inspection. 
So, if it has a dot or corner chamfer that's what I put on the silkscreen legend, and some numbers if possible on connectors to help assembly and service.
With diodes, I try to put a small diode symbol near the part if I can or on the assembly layer, right on top of the component if there is no room to show it on the printed legend.
Actual pins on components, I use BCE, GSD or AK rather than pin numbers having been caught out in the past with how the device manufacturers seem to switch these around.
(more than 3! combinations for sot23s for example)

Regards,
Phil Dutton CID+
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