I know you can get the list of the processes running in tasklist.exe, but I want to only get the applications running.
Like only these programs:
Instead of all the programs in "Processes"
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Windows uses their own criteria to determine which processes to place in the Applications tab. I'm not sure it's even freely available.
What you can do is use tasklist.exe /v /fo csv.
/v gives you verbose. /fo csv makes it so you can split on commas for easy parsing in java.
The window title column will let you know the title that would appear if there was a window. The session name lets you know if it's a background service or a console (although some consoles run in the background without you seeing them). From there you'll have to come up with your own criteria for what you want to consider an application and what you want to disregard as a background process.