Every time I start/stop/redeploy my Tomcat Server (or Glassfish) or something like that, eclipse ask if it should save that SQL Scrapbook file.
But I do not want to save it, because it contains only some “temporary” queries. So I press “No”. But for the next server start it ask again and again.
So my question is: Is it possible to suppress this question for SQL Scrapbook files?

You might achieve some measure of what you want by enabling “autosave” in General->Workspace “Save automatically before build”. By having the file saved you will not get prompted. However since this would affect all files you’re currently working on; it’s probably not what you want.
What you want may not be possible.