I have a laptop with Synaptics touchpad, and one of the biggest annoyances in its implementation is how the "wheel" strips act upon the GUI element where the mouse is pointing regardless of the current focus. It took years to beat focus-follow-mouse people into a marginal submission, yet they still find every crack to seep through, like kerosene. Naturally, this behaviour is not tunable.
Another retardity in this area is the behaviour of the panel. Some genious came up with an awesome idea to flip windows if panel receives a wheel click. The problem with that is, a strip on the laptop is difficult to make to deliver just one click, so the function is useless to me. Also, it is too easy to hit the strip accidentially (which would not be a big deal if not for the enforced focus-follow). So, for one reason or the other, I would like to disable this behaviour. I don't even want to seek excuses for this wish. Just do it. But it's impossible.
So far the only group that displayed a clue in this was, strangely enough, Mozilla. They fixed bugs I filed and in general had an understanding of various input and display technologies, despite only being browser people. You'd think desktop developers would know how a touchpad differs from a wheel mouse.
UPDATE: Chris pointed out in comments that a fundamental reason exists why wheel behaves this way: the extra button events are mouse buttons, and those go where pointer points. I knew it, but it didn't click. I still think that applications should be able to work around this, although perhaps at the cost of some extra events being delivered.