Check out Dexpot. It's in the forums. Use the transparency feature "define colours". The fonts don't render nicely or more accurately I haven't figured out how to improve that but, it achieves relative full transparency on the internal window.
Here's a screen sample.
You could use a program called 'Shell Enhancer'. It's one of those swiss army knives of desktop customisation aka Does a load of different things. One of the things it does do is make any window (Either by Application or Title name) transparent. The window can be set to fully transparent or partially (It works with a slider).
The transparency effect is a little hidden so ill give you a heads up :
After you've installed the app, Start it and right click on it's Icon in Systray and choose Settings > Settings. Then Go to the AUto Managed Tab. Click on the Add icon and you should get a wizard dialouge. choose the app you want to make transparent ans click next. Make sure 'Allow X-Window style moving/resizing' is checked then click next. check 'colour key' and move the mouse over the picker, left click and drag it over the notepad window untill it turns into the same colour as the picker colour tab. then select the 'Transparent' option and the amount of transparency you want the window to have (0= Fully transparent). Click Next and then finish.
Restart notepad (Or your app of choice) and you should have a window with a transparent background. I've noticed that on apps like notepad when you type there is an issue that appears only sometimes with the text. It sometimes renders incorrectly but this could be because of the fact that my graphics card is not very powerful.
Hope that helped.
shellhancer can be had here :
Aqua-Soft Forums