Here's some code to clean up a freshly unpacked minecraft.jar that will delete all .class files and remove the following folders:
com, lang, net, paulscode, META-INF
* If META-INF isn't there, it'll say something like "Cannot find file specified", just ignore that.

Create a new text file with this code and save it with the extension .bat. (mc_texturepack_new.bat for example).
This is called a 'Batch' file. Place this file in a freshly extracted minecraft.jar folder and run it.

--- Copy text below this line ---
@ECHO OFF
ECHO This file will delete all .class files and remove the following folders:
ECHO com, lang, net, paulscode
ECHO _
ECHO Close the box if you no NOT want this.
pause
del *.class
rd /Q /S com
rd /Q /S lang
rd /Q /S net
rd /Q /S paulscode
rd /Q /S META-INF
ECHO _
ECHO Done.
pause
--- Copy text above this line ---

Notes on the commands:
@ECHO OFF
Commands and text will show up in the command window if this is not off.
ECHO
Display any text typed after this, within the same line. "ECHO _" is used because you cannot echo a blank line.
pause
Wait for a key to be pressed before continuing
del
Delete a file - use del /? to get help
rd
Remove Directory - removes a folder or tree (subfolders), use rd /? to get help
' * '
Asterix means everything so *.png would mean all files with .png extension, and yourmom.* is all forms of yourmom.