Better control over Emacs windows

Question

I spend a lot of my time in emacs, and for the most part it's wonderful. But one thing really drives me nuts when I'm deep in it, and that's control over which window various new buffers are opened in. When I do find-file, it always opens in the current window, and this is what I like. But tons of other modes like to split my windows for me, change the layout, and do various other things that annoy me. For example running M-x manual-entry seems to have no rhyme or reason about where it opens the manpage, and various org-mode commands do the same thing, closing windows I want to keep open, etc. I don't like having to redo my layout everytime I want to look at my org agenda or open a manpage.

In short, is there anyway to globally control which windows are used for modes that want to open in a window other than the current one? Can I direct them more easily? Or will I have to hack each mode to act the way I want it to?