Version 3.0 although fully functional and stable is still a beta.
If you prefer you can still download Version 2 below.

Download Version 3.0 Release Candidate 2 (extract the zip and run "runsc.exe")

Whats New in Version 3.0

Completely rewritten.
No longer is dependant on .NET so it is now completely portable.
Easier to use for the "average" user,..
-The Shortcut Name, Icon, Working Directory, and Version information are automatically populated when you browse for the shortcut path.

History

3.0.0.2 Release Candidate 2
Fixed issue with Shortcut Name and Version Number population when creating a shortcut for compiled .bat files.
3.0.0.1 Release Candidate 1
Fixed temp directory selection in advanced options.
Fixed temporary files not being deleted
Fixed issue if temp directory changed mid process.
2.99.0.3
Rearranged the interface a little.
Grouped the configure and create buttons.
Simplified a couple options.
Added some field validation to make sure there is at least a name and path.
2.99.0.2 {first beta release}
Rearranged the interface.
Added additional functionality,..
The shortcut name, icon, working directory, and version fields are automatically populated when you browse for the exe.

Shortcut Creator 4U3 VB .NET:
You MUST have .NET 1.1 installed to use the .NET version of this utility.
You can download .NET 1.1 through windows update or manually HERE.
Download Shortcut Creator 4U3 (written in VB.NET)
Download Shortcut Creator VB.NET Source

Don't have .NET installed? Try the New Version 3.0 above.

2.0.20.0
Added a browse button to the temp files option.
Added an autorun checkbox (now you can make the shortcut autorun with launchpad)

2.0.19.0
Added temp files location to the advanced options, now you can choose what directory the shortcut creator uses for temporary files.

2.0.18.0
Added AppStopCMD
Added AppStopCMD working Directory
Added AppStopCMD argument
Rearranged advanced options

2.0.16.0
Moved advanced options
Added Version field to advanced options
Added temp files field to advanced options
Disabled buttons unless Shortcut Name and Application Path are populated
Changed default run folder for run only option, now uses same folder the setup is run from

2.0.14.0
Added Argument option

2.0.13.0
Fixed an issue with incorrect format in the appStart cmd

2.0.12.0
Added the help file

2.0.11.0
Fixed issue with spaces in shortcut name.

2.0.10.0
Fixed issue with VB6 code left behind.

2.0.8.0
Fixed issue with working directory selection.

2.0.6.0
Should be feature complete with the exception of the help button.

Known Issues:
The help file has a broken image link.
An update is available as a seperate download above.

Shortcut Creator 4U3 VB6:
The VB6 version was never fully completed.
I will not be updating it, it is here only for "historic purposes".
Shortcut Creator VB6 (written in VB6)
VB6 Source