When I use Play on Linux i found that i have to install programs such as Ventrilo, Firefox and some other programs for multiple prefixes.

I think it would be a benefit to have Play on Linux application setup like so.

+World Of warcraft
- Wow.exe
- Firefox
- Curse
- Ventrilo

+ Steam
- Firefox
- Steam
- Ventrilo

+ <Prefix>
- <.exe>

Maybe not like a file tree but maybe folders or some easier method at getting to the exes i want to use and not have 2-3 Ventrilo executables or 2-3 Firefox executables

I know what you mean, I had to install WINE Gecko for almost every app I installed

Well unfortunately, due to the nature of wine, installing programs multiple times isn't something that can be avoided, but theythinki does have a point. There should be some sort of organization to allow users to tell the difference between the different programs installed in each different prefix, especially if they're different instances of the same program.