Shaped skinning is hard,you have to take into account all the padding and think of stuff like a grid.
Padding is the messengers way of saying how many pixels an object/s needs to be pushed in from the Left, Top, Right and Bottom I'm sure you've encountered it already.
Willz iron man/batman/whatever basically removes a chunk of the rectangle of messenger shaped like whatever, he sets it with UMargins so that those parts of messenger are not stretched when messenger is reszed, he tells messenger to remove those shapes from each corner, as you would see if you looked at his SkinInfo.xml
Then in messenger his background matches the shapes that have been taken out so it looks like it's natural and fits.
But of course messenger still thinks the borders are on the exact outside, so you need to adjust the borders (this is all in the documentation) telling it to come in by 15 pixels etc.
Honestly mate the best thing is to just look at examples of the skins you like and try to do something similar with a new skin based on the examples code.
How about this: Try making a skin shaped like a war medal
You'll need to subtract the corners with images with a shape like this (rotating as necessary)
___
| |
___/ |
|_______|
Then play about with the padding in the definitions, till everything is visible again and not cut out. From memory it'll be the window icon and text, minmaxclosebar, possibly the display picture, display name, status, personal message bar, dashboard, then the bottom of the contact list.
This is a fairly simple exercise and you'll learn a lot, good shaped skinning currently IS HARD! Don't be fooled, ever think that there's more than likely a reason there are very few if any shaped skins in the database.