Edit: I am completely re-writing this guide to make it easier, more pictures, and more functionality.
So, have you wanted to create your own winterboard theme?
Well, this is the guide for you!
What you need;
1. An iPad. (isn't that obvious?)
2. Be Jailbroken>>>>>>>>>>>> iPad 2: TUTORIAL - Jailbreak the iPad2 on 5.0.1 with Absinthe
>>>>>>>>>>>> iPad 1: TUTORIAL - Jailbreak iPad1 on IOS5 using redsn0w
3. Download iFile from Cydia. (Preferably the paid version)
4. Download WinterBoard from Cydia.
5. 30 minutes or so. (depending on your knowledge of iFile and the general iPadness)
Let's get started! (Guide written with the iPad in Landscape)
1. Open iFile and navigate to Var / stash and scroll down to the folder named "Theme.(whatever)"
2. Tap "edit" in the top-right hand corner.
3. Tap the + icon on the bottom leftish.
4. Name the folder whatever you want. Then add ".theme" to the end of your folder name.
5. Tap "create" in the top of the window. Then tap "done" where the edit button was.
6. Open the folder you created, and repeat steps 2-5 but don't include .theme and name the folder "Bundles"
7. Now, this is where you will create custom theme stuff for each app. So, figure out which app you want to theme first.
After you know which app you want to theme first, on iFile, tap "Disk" on the left. Navagate to var/mobile/Applications.
8. If you have the paid version of iFile, tap on the gear icon in the bottom left. In that window that pops up, turn on "Application Names". Then just tap back in the main part and the window will disappear.
9. Now, all the folders show the app titles, instead of the wierd code thing. Tap on the app you want to open it. I will use Facebook as the example
10. Open the Facebook folder and tap on "Facebook.app". This is where all the resources for the Facebook app are stored.
11. Scroll down and look at all the pictures that make up the Facebook app. Now, you could make changes to the Facebook stuff here, but if you screw anything up, then you have to delete and reinstall the Facebook app. Winterboard takes all the hassle out of theming because if you screw something up, then you don't have to worry.
But, anyway, these are all the pictures you can replace with your own stuff to make a theme.
12. Scroll down to the Info.plist. Tap on and open it with the text viewer. Look at the line below "CFBundleIdentifier". That is the springboard identifier for that app. For example, the one for Facebook is "com.facebook.Facebook". Remeber that for the app you want to theme.
13. Go back to var/stash/Themes.(whatever)/the theme you created/Bundles
14. Now create a folder with the CFBundleIdentifier you remembered from earlier. So, the example was com.facebook.Facebook.
15. Now, first lets create a new icon for facebook. The icon file for all apps is labeled "Icon-72.png". So find a picture! Google, Photoshop, your family albums.... whatever. But, whatever you use, it must be 72x72! If not, the iPad WILL IMPLODE! (nah... Just kidding) But, make sure they are 72x72 and they are in .png format.
16. So, find your pic, and get it to that folder somehow, (SSH, whatever) and rename it Icon-72.png.
17. If you go back to the app folder, any of the pictures you see you can replace with one of your own. So, the same way as the Icon, any of those pictures can be themed. Just make sure they are the same size as the original picture. So, Photoshop is very helpful.
Just remember, any pictures you used, you have to have proper permission for to send your theme to a repository.
Look here to submit your theme to Cydia! How to: Submit Your Theme to Cydia!
Post any questions and I will try my best to answer!