How to always open new files in the top window of an already running instance of an application on OS X?

Question

I run OS X Mountain Lion and open files in four ways:

• the Finder
• Alfred file search
• the open command typed directly into the shell
• shell scripts that run open and are triggered by applications like Alfred or Keymando

My primary editor is MacVim. I observe that sometimes when I open a file, it opens in the current window of MacVim. In other instances, it will open a new window. There is a similar phenomenon when running web searches from Alfred. Sometimes, a new tab will open up in a preexisting Safari window; other times it opens in an entirely new window. In Safari preferences, I have "open pages in tabs instead of windows" set to "Always".

I can't figure out what the pattern is here. Can anybody explain how it is that the system decides whether to open in a new or preexisting window, and how to make it always use the preexisting one?