I am pro-Mouseover scroll wheel. Among the mouseover based, there are two camps. Those that ignore the wheel when the mouseover doesn't make sense, and those that use the focus when the mouseover doesn't make sense. I agree with the later.
Mouseover based: Uses mouse location to decide what the scroll wheel means.
Firefox v3.5.5 Tabs vs Window
Picasa 3 v3.5.0 Explorer vs Picture list
Calibre v0.6.7 Content vs Detail
TextPad v5.2.0 Explorer vs Content
Photoshop v8.0 Picture vs Picture
Google Earth v5.0.11733.9347 Left Menu vs The Planet >.<
FreeMind v0.8.1 Content vs Notes
Focused based: Uses the application focus to decide what the scroll wheel means.
Visual Studio '05 v8.0.50727.42
Windows Explorer XP Pro SP3
Dreamweaver MX v6.0