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Mouse wheel should scroll the widget under the mouse pointer, not the widget with focus. All Mozilla apps scrolls the widget under the pointer, and it's the standard behaviour in all Java Swing applications. I know that bug 45355 is closed, but I think this is a very important bug that needs to be fixed. Please consider this issue again.
But Word and IE do not. Word and IE are more representative of native applications on Windows than Mozilla and Swing.
I just tried the mouse wheel in Word 2002 on my W2k system. It scrolls the window under the pointer, open the outline view (I run a swedish word version so I don't know if that's the correct name) and try. Internet Explorer 6 seems to work differently, sometimes it only scrolls the widget if it has focus AND the mouse pointer is above the widget. This can be tested by opening the explorer bar. Regardless, I think this is a big disadvantage for Eclipse compared to Swing IDE's like Intellij, and I don't see why you at least can make the mouse wheel behaviour configurable.
I find it increasing annoying that I actually have to click on a view to get it to scroll. This is a big usability/accessibility loss.
Another example of an MS app that works this way is outlook express. You can scroll one window while the focus is in another. Vey handy for reading news.
*** This bug has been marked as a duplicate of 75766 ***