My very favorite tool in Media Composer and Symphony is Animatte. I use it in every project, from custom transitions to just hiding stuff or changing the layer order of composites.
Here is a small sample step-by-step technique for creating custom transitions using Animatte. I hope that this example gives you a small idea of why I find this tool so usefull.
Note: For those of you without Animatte, just export your two clips into Adobe After Effects or Discreet Combustion and follow the steps (minus nests) with an animated mask.
The first thing you want to do is matchframe the outgoing clip and place a snippet of it on the track above the one you're working with.

Some actions do not require a reposition effect at all -- i.e., a person walking by, a truck passing, etc.
This one does need a reposition effect to take the Blue Mouth candy package away. Make sure that your first keyframe keeps it static until the underlying dissolve is finished. You can then just make a keyframe to pan or tilt it out of the screen.

Now you are ready to auto-nest your animatte effect. 'Alt-drag' it on and use the Poly Tool to simply trace around the object you want to cut out. You only have two keyframes used by reposition that you need to match. If you used acceleration in the reposition, use it with the animatte's position/size as well. Add a little feather to its edge to help it blend or to hide imperfections.

Now you have a cool transition that doesn't have that cookie-cutter flavor like most packaged transitions have. It's your own and it's obvious. Maybe a little too obvious right now so I'll add a layer of blur as filler to smooth things out just a bit.

There you go -- a custom transition that took only a couple of minutes to create. The possibilities are endless, really. A little creativity will find a use for Animatte in every project.
Here is the finished transition:
Click here to see the finished transition
-- Grinner
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