Unnecessary files/folders added when installing software.

I recently installed infrarecorder and WinRAR on my flash drive. When these programs were installed, there were shortcuts added to:

C:\ProgramData\Microsoft\Windows\Start Menu\Programs\InfraRecorder

and...

C:\Users\User Name\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\WinRAR

These shortcuts show up under All Programs in the Start Menu. I plan on using the program strictly from the flash drive, so I want to delete the folders the installations made. Are there any other locations I should look that programs will typically add folders to I may not want on my internal hard drive? or is this about it?

Also, why were the folders added to 2 different locations, both for adding shortcuts to the start menu.

There is a location for installing shorcuts on the start menu and on the desk top "for all users" and then there is a place to put them for your own user account only.

Which place they go is sometimes up to the person installing (Ever been asked "Install for all users or just yourself?") and sometimes installers just choose one or the other without asking.

I see. Are there any other possible files and folder an installation may produce? Perhaps even in a less obvious place like where my start menu program shortcuts are put?