Tabs opening in a minimised safari window, not the active one I’m often using multiple windows in Safari minimizing the windows I’m not working in. However, when I click on a link i.e. in Mail it opens it not in the active window but in the minimized one instead (the one that has been created first after opening the Safari).

How can I set the Safari to open links in the currently active window, not a minimized one?
I believe the default behavior of Safari is to open a link in the oldest open window. Minimized windows tend to get old, hence the annoyance of Safari bringing up minimized windows when opening a link from another app.

You can easily test this. Wait for it to happen. Then re-minimize the window. The behavior should be repeatable infinitely. Next copy the URL of the window you want minimized and close that window. Open a new window, paste the URL, hit return, and minimize it. Then open the external link and it will no longer go to that window.

Of course this doesn't help - it just explains the behavior. The only thing that might eventually help is filing a bug report:

http://www.apple.com/feedback/safari.html