With VMWare ThinApp AppLink you can create multiple "ThinApped" packages and tie them together via AppLink for easy upgrades and maintenance of application dependencies while saving yourself the time of going through multiple installs of the same dependencies across multiple applications. 

Here is how to package one of the more common application dependencies.  The .Net Framework.  This can also be applied (without the extra steps as well to Adobe, Flash, Office, etc...).<!--more-->
<ol>
	<li> Start with a clean Capture and Build Machine in VMWare Workstation.</li>
	<li>Run the ThinApp Capture process.</li>
	<li>Minimize or Close the ThinApp Capture Window (don't worry, ThinApp will restart after the reboot .Net Framework requires).</li>
	<li>Install the .Net 2.0 FrameWork.</li>
	<li>Once Complete, Install the recommended .Net 2.0 Framework and Windows Updates.</li>
	<li>Shutdown the .Net 2.0 Framework Service.</li>
	<li>Run the ThinApp Post Install Capture to populate the captures folder in the directory you choose.</li>
	<li>Clean up the Captures Folder by performing steps 9-15.  Thanks to the vmware blog for following steps... <a href="http://blogs.vmware.com/thinapp/2008/11/step-by-step-in.html">http://blogs.vmware.com/thinapp/2008/11/step-by-step-in.html</a></li>
	<li>Delete the <strong>%Cookies%</strong> folder and all subfolders and files.</li>
	<li>Delete the <strong>%drive_C%</strong> folder and all subfolders and files.</li>
	<li>Delete the <strong>%History%</strong> folder and all subfolders and files.</li>
	<li>Delete the <strong>%Internet Cache%</strong> folder and all subfolders and files.</li>
	<li>Delete the <strong>%Profile%</strong> folder and all subfolders and files.</li>
	<li>Any subfolder of the <strong>%SystemRoot%</strong> folder which starts with a "$" sign.
Example: <strong>%SystemRoot%$NtUninstallWIC$</strong>
NOTE: Don't delete the %SystemRoot% folder or files, just the folder(s) which start with the $ sign.</li>
	<li>Delete the <strong>%SystemRoot%LastGood</strong> folder and its subfolders and files.
NOTE: You may need to reset file/folder attributes and/or delete each item one at a time.</li>
	<li>Make additional configuration changes as necessary.</li>
	<li>Build and Deploy the Application Package.</li>
</ol>
After this you should have a working Package to use AppLink from your applications to associate the .Net Framework!

Stay tuned for how to configure AppLink to add the Framework and other dependencies to your applications.