Ok, so you need to back-up your 3rd Party Apps: a) because you want to or B) because you are about to wipe your device. Well, heres a How-To to get the job done. Here we go:
1)Download & install the newest Desktop Manager Version
HERE 2) Connect BB
3) Open DM
4) Select Switch Device Wizard
5) Select Switch BB Devices
6) Select Next
7) Select USB & then your PIN #
8) Select Next. Enter your Password if required
9) Uncheck User Data & Settings and also Include Messages so that only 3rd Party Apps is selected
10) Select Next
11) When it's done backing up leave the screen as is.
DO NOT select Next or Cancel
12) Search your computer Folders & Files for a folder with your PIN # as the name.
DEFINITELY check System Files & Hidden Files as well
13) After you find it, copy it &
SAVE it to a easy accessible place
14) Go back to the Switch Device Wizard page that we left alone & cancel it.
ALSO, check and make sure the folder
IS saved before Canceling or the folder will be
LOST 15) You can now wipe the device with
JL_Cmder RESTORATION 1) After you've loaded the OS go back & run the Apploader & Select ADD
2) "Browse" to find the folder we saved with your PIN # and Double click on the file named yourpin.alx.
3) Your 3rd Party Apps should appear in the Apploader screen
4) Select Finish to load Apps to device
5) Now you may restore other data from a previous backup.
***UPDATE FOR DM 4.7*** 1) Plug in device>Open DM>Device Switch Wizard
2) DSW>BlackBerry devices
3) Make sure
ONLY 3rd Party Applications is checked>Select Next
4) DM will back up 3rd party apps, when finished
DO NOT select Next or Cancel!!! 5) Search your computer Files & Folders and
DEFINITELY make sure to search
HIDDEN FILES & FOLDERS for a folder with the same name as your PIN and a .alx file.
6) Move both the folder and .alx file to an easy a
accessible place you remember.
7) Go back to the DM and cancel the process.
PIN Folder- Search Method for VISTA Users 1) Click Start Circle
2) Click on Help & Support
3) Enter "Search Folder"
4) Click on "Find a file or folder"
5) Click on "To find a file or folder using the Search folder"
6) Click on "Click to open search"
7) Click on the expand arrow next to "Advanced Search"
8) Click on "Location" and use Local Disk C: (usually!)
9) Enter the PIN of your BB under "Name"
10) Make sure the box is checked next to "Include non-indexed, hidden, and system files"
If you do not want to follow those instructions you may take this path also:
C:\Users\[name]\AppData\Local\Temp Thanks to jfksabal for the Vista search process. RESTORE PROCESS 1) Plug in device>Open Desktop Manager
2) Select Apploader>Add/Remove Applications
3) Select Add
4) Browse to Folder named your PIN #
5) Select the .alx file and Select Open>Select Next
This Tutorial was made by Crucial_Xtreme. Please do not copy and paste this tutorial anywhere without my permission. You may however, post links. Thank you very much and I hope this helps atleast one person. 
**Updated**How To Back-up 3rd Party Applications**Updated 
Not active, busy with work 
Linear Mode
