The strength of the wind generated by Gust of Wind is sufficient to disperse any of the cloud type spells. My question is does it disperse them completely, or only in its area of effect (a line)?
I would say in a line. Unfortunately there is no mention of using gust of wind to clear out cloud spells. (You would think they would address it as a common tactic against clouds.) The closest analog I could find (in the SRD) is using area affect fire spells against Obscuring mist which says that it only affects the area of effect and not the entire mist.
I would rule it clears out that line and the cloud does not fill in except for maybe(off the top of my head) cloudkill which has movement Though I would reduce the volume of the cloudkill by the amount of cloudkill that was wiped out by the gust of wind. Magic gives the cloud its shape and gives it a set volume. That Volume still exist technically at the end of that 60 line. so it is not destroyed just moved.
By the RAW the gust of wind effects a line and nothing else.
Since it is magical wind it ignores physics etc and doesn't create a vacumn effect by blowing along so only that line is cleared.
It still makes it a useful spell without destroying the cloud spells. I think you need something like weather control that affects the entire area before you can just blow away the cloud.
Looks like time to research greater Gust of wind and make it a nice cone shape.