For emergency patches:
If this is just a code file, I copy the whole / bin / out and replace the whole DLL (mostly out of habit)
If its aspx, I just copy aspx.
For real deployments, I have an automated system that checks the code from the source control, builds a clean version of the assembly, shuts down the site, and then copies its deployment targets. Its a one-click process (thanks CruiseControl!).
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