[Touch Pro, Fuze Themes and Apps] Mandragore:
Try the Sashimi application to save files and registry settings and restore them manually or automatically. It may have a steep learning curve, but once you've put in the effort, it saves you much more time in the long run. Have a look at the contents of my Sashimi filebackup.ini and regexport.ini to get an idea. Good luck!

Filebackup.ini

[Applications]

FileBackupDirMode=Auto

StartUp=\Windows\StartUp\*.*

changeScreen=\Windows\changeScreen.config

AEBPlus=\Program Files\AEBPlus\AEBPlus.cfg

TaskFacade=\Program Files\TaskFacade\settings.xml

TouchLockPro=\Program Files\TouchLockPro\TouchLockPro.xml

Lumos=\Program Files\Lumos\settings.txt

ET9=\Windows\ET9*.*

[Opera9]

FileBackupDirMode=Auto

Secure=\Windows\Opera9\secure\wand.dat

Skin=\Windows\Opera9\Skin\*.*

Cookies=\Windows\Opera9\cookies4.dat

Bookmarks=\Windows\Opera9\opera6.adr

Settings=\Windows\Opera9\opera.ini

Regexport.ini

[MySettings]

RegExportDirMode = Auto

JPG1=HKCR\.jpg

JPG2=HKCR\JPG-File

WMV1=HKCR\.wmv

WMV2=HKCR\wmv-file

Notifications=HKCU\ControlPanel\Notifications

Sounds=HKCU\ControlPanel\Sounds

SoundCategories=HKCU\ControlPanel\SoundCategories

Phone=HKCU\ControlPanel\Notifications\Phone

SIP=HKCU\ControlPanel\SIP

RIL=HKLM\Drivers\BuiltIn\RIL

Inbox=HKCU\Software\Microsoft\Inbox

Messaging=HKLM\System\Inbox\Settings\PropertyPath

Attachments=HKLM\System\Inbox\Settings\AttachPath

Backlight=HKCU\ControlPanel\Backlight

GSensor=HKLM\drivers\builtin\gsensor

Identity=HKLM\Ident

BlueTooth=HKCU\Software\Microsoft\Bluetooth\Settings

BlueToothDevice=HKLM\Software\Microsoft\Bluetooth\Device\001ad5f020cc

BlueToothSerives=HKLM\Software\Microsoft\Bluetooth\Services\0000110B-0000-1000-8000-00805F9B34FB

Signature=HKLM\Software\HTC\Signature

Power=HKLM\System\CurrentControlSet\Control\Power

PressureThreshold=HKLM\Drivers\TouchPanel\PressureThreshold

FingerPressure=HKLM\Software\OEM\TFLOSettings

ClearType=HKLM\System\GDI\ClearTypeSettings

ShellFolders=HKLM\System\Explorer\Shell Folders

GPS=HKLM\SYSTEM\CurrentControlSet\GPS Intermediate Driver

TCPWindowsSize=HKLM\Comm\tcpip\Parms\TcpWindowSize

BitmapCacheSize=HKCU\Software\Microsoft\Terminal Server Client\BitmapCacheSize

Wallpaper=HKCU\ControlPanel\Desktop

[HTC Software]

RegExportDirMode = Auto

ProgramLauncher=HKLM\Software\HTC\Manila\ProgramLauncher

HomeLSKPath=HKLM\Software\HTC\Manila\HomeLSKPath

HomeLSKArguments=HKLM\Software\HTC\Manila\HomeLSKArguments

HomeLSKText=HKLM\Software\HTC\Manila\HomeLSKText

HomeRSKPath=HKLM\Software\HTC\Manila\HomeRSKPath

HomeRSKArguments=HKLM\Software\HTC\Manila\HomeRSKArguments

HomeRSKText=HKLM\Software\HTC\Manila\HomeRSKText

AccountManager=HKLM\Software\HTC\HTCAccountManager

Camera=HKCU\Software\HTC\Camera

SmartTouch=HKLM\Software\HTC\SmartTouch

StartUpAnimation=HKLM\Software\HTC\HTCAnimation

TaskManager=HKCU\Software\HTC\TaskManager

AudioBooster=HKLM\Software\HTC\AudioBooster

HSUPA=HKLM\Software\HTC\AdvancedNetwork

AudioManager=HKLM\Software\HTC\AudioManager_Eng

Album=HKLM\Software\HTC\HTCAlbum

Animation=HKLM\Software\HTC\HTCAnimation

YouTube=HKLM\Software\HTC\YouTube

[MySoftwareHKCU]

RegExportDirMode = Auto

QuickMenu=HKCU\Software\AlenSoft

TotalCommander=HKCU\Software\Ghisler

PIM=HKCU\Software\FdcSoft

Changescreen=HKCU\Software\idevelopstuff

RSS=HKCU\Software\Ilium Software

MobilePad=HKCU\Software\MobilePad

Modaco=HKCU\Software\Modaco

Mort=HKCU\Software\Mort

RAR=HKCU\Software\RAR

SK=HKCU\Software\sk

VisualGPSce=HKCU\Software\VGPS

TouchLockPro=HKCU\Software\ZuinigeRijder

MediaPlayer=HKCU\System\State\MediaPlayer.

cleanRAM=HKCU\Software\HTCAddicts\cleanRAM

ClearTemp=HKCU\Software\VicSoft\ClearTemp

Taiyoukei=HKCU\Software\RBSoft

[MySoftwareHKCM]

RegExportDirMode = Auto

Adobe=HKLM\Software\Adobe

AdvancedConfig=HKLM\Software\AdvancedConfig

CorePlayer=HKLM\Software\CorePlayer

IE=HKCM\Software\Microsoft\Internet Explorer

MediaPlayer=HKLM\Software\Microsoft\mediaplayer

ShellKeys=HKLM\Software\Microsoft\shell\keys

Navigon=HKLM\Software\Navigon

SRS=HKLM\Software\SRS

PocketShield=HKLM\Software\PocketShield

eT9=HKLM\Software\Tegic\eT9

nueDynamicClock=HKLM\Software\Wei Enterprises

TouchInCallScreen=HKLM\Software\Marzens