Tools that everyone should know about to make themes. Here is some that I use. Feel free to add to the list.
7-zip - 7-Zip Great tools for opening .apks and extracting them with out changing the extension.
ADB - See Android SDK
Apk Manager - Apk Manager 4.9 - Makes Modifying Ur Apk A Breeze (Windows/Linux) - xda-developers thanks to Rola, I love this tool. All in one for decompile, compile, sigin, and pushing to the phone.
apktool.jar - Downloads - android-apktool - Project Hosting on Google Code If you using windows you need the top two downloads.
axmlprinter2.jar - AXMLPrinter2.jar - android4me - Prints XML document from binary XML file (with correct namespace handing & attribute formatting). - Project Hosting on Google Code= There is a GUI format as well here Android XML Decompiler - Android @ MoDaCo
Android SDK - Android SDK | Android Developers Many useful tools within this package.
Colorchangev3.jar - http://forum.xda-developers.com/showthread.php?t=535630 used for changing notification text (clock, date, ticker and so on )
HxD - Downloads | mh-nexus Useful for doing hex edits if you can't get apktool.jar to work.
draw9patch.bat - In the tools folder of the Android SDK.
Eclipse - http://www.eclipse.org/downloads/ Download eclipse classic.
xUltimate tools - [Release] xUltimate Awesome tools by X.
Change "M" logo - Droid 1 custom bootloader logos to replace Motorola logo , Just wanted to add this in case people wanted to make one to go with there theme.
Again this is just a list of tools used for theming.