When minimizing, not have new window of same app come to focus There's a couple of behavior's that I find very frustrating, and no luck yet in fixing them:

Imagine chrome with multiple windows open.  There's one in front, then another application, then the other chrome windows.  When I hit apple + M to minimize, another chrome window pops up, rather than showing me the other application, which would be desired.

Similarly, if I have chrome windows on multiple desktops.  If I'm using one application on the first desktop, go use chrome on the second, and switch back to the first, chrome will appear on top when all I want is the original application!

The wrong window appears on the foreground in leopard.

Thoughts? Thanks!
Have you considered using CMD-H to hide the application instead of minimize it? If you minimize a window, the app that owns that window is still the focused app, but if you hide an application, it will change focus to the next app in the switcher. 

I can't help with the second part of your question. I assign apps to spaces so they don't clutter my spaces (even though they do sometimes - I'm looking at you, Photoshop).