"I love the fact that OS X will scroll the window that the mouse is hovering over, even if another application has focus. That way I can scroll an example that I am coding in TextMate without having to lose keyboard control on TM"
This also happens on Windows (at least on Chrome) but Windows goes even further: you can click through a link or button on a non-focused window. On OS X, in order to follow a link or click a button on some non-focused window, you need to activate it by clicking and then click again on the desired link/button. This drives me nuts as I found out I use this all the time on Windows. I call this feature "smart focus".
Command click on buttons in background windows to click them without bringing the window to the front. Works for most things (at least anything using standard cocoa controls), although clicking links in Safari is a notable exception since it still seems to bring the window to the front.
You can also command+click and drag background title bars to move those windows without bringing them to the front.
It's a good workaround I guess. I'm still not sure which way is the best. OS X kinda prevents the user from misclicking outside the window while Windows doesn't but if you're in need of some speed (and fewer clicks/keys) then you might prefer the Windows way.
This happens between Chrome windows, because you are still within Chrome if you have one of the windows in focus, so Chrome can determine which window you want to scroll by figuring out which one you are hovered over. On Mac, it scrolls even if the application in question is out of focus.
It's called "click through" and I also prefer the Windows behavior. Especially since the behavior is not consistent on Mac OS: certain actions do not require a click through (e.g. you can close a window in the back without bringing it on the front).
"Windows goes even further: you can click through a link or button on a non-focused window."
This is a interaction design mistake. On Windows, if you click inside an unfocused window you can perform an action otherwise unintended, Mac OS X's way and Haiku's (www.haiku-os.org) is correct. Interestingly Firefox follows the Mac way, but on at least Windows Chrome does not, and if you happen to unintentionally select the close tab button, you're tab close and if you're in Incognito mode, you lose that tab because there is no history.
I understand your point of view but just because you might do something by accident it doesn't mean it's a design mistake. There's some advantage for each method, I prefer to make a mistake a day a week than being forced to click twice everytime I'm using side-by-side windows (like when I'm writing code and testing).
Inconsistent click-through behavior is a major problem of OS X. (Gruber has written pages about it.) I don’t think it matters whether click-through is possible or not – your preferences will just depend on what you are used to – but the behavior should at least be consistent. In OS X, it is not.
This also happens on Windows (at least on Chrome) but Windows goes even further: you can click through a link or button on a non-focused window. On OS X, in order to follow a link or click a button on some non-focused window, you need to activate it by clicking and then click again on the desired link/button. This drives me nuts as I found out I use this all the time on Windows. I call this feature "smart focus".