To do what GG is talking about, the magic is in cutting and pasting keyframes between the two clips filter/motion windows.
Example:
Put two clips up to each other on the timeline.
Take your first clip, add the wave filter to it. In the wave filter window, drag the only keyframe to near the end of the clip. Now move the cursor/bar to the end of the clip. Adj. settings to tweek picture. This will create a new keyframe. Right click on this new/last keyframe and select COPY. Now add a wave
filter to your second clip. Drag the only keyframe away from start of clip. Move cursor/bar to beginning of clip then right click and select copy.
You now have a custom transition. Adjust space between keyframes to affect transtion duration. They don't have to be the same for both clips.

Or use the same idea and apply it as a Track Level FX. Same for Motion. I just realized that this would be faster. No copying and pasteing of keyframes this way.
Oh yeah, this is a major score. ; )
Duh, don't know why I didn't think of this before.
I can see times when you would need to do it at a clip level though.
Lesson, many ways to do the same things in Vegas. FX filters can be at clip, track or final output. Motion at clip and track level.

You can add a stock transtion to smooth out the hard cut inside your custom transtion.

Duration can be linear or dynamic.

The new deform filter in Vegas 3 is gold. Anybody looking for 3D transtions? You got em now.

Cheers,
Craig H.