I would like to be able to remove references to a particular, individual package in a repository.
If I do not want install something it would be nice to speed up apt-get update(by skipping those) and have a cleaner synaptic screen.
If I understand you correctly, I don't believe that you can remove entries, or prevent them from showing up in Synaptic Package Manager without removing or disabling your repositories.
However, you can create custom filters based on a variety of criteria:
Create a new filter (and name it accordingly).
Define your filter(s) based on three criteria:
Status of package
Section
Graphics
category, for example.Properties
Return to the main Synaptic window and click the Custom Filters
button and then select your newly named filter.