Google Chrome has a feature called App Launcher. If you install any apps from that part of the store the browser will put shims for the apps in ~/Applications (it also puts an identical copy in ~/Library/Application Support/Google/Chrome/Default/Web Applications/LONG_RANDOM_IDENTIFIER/). If it is doing this then you should have a folder within ~/Applications called "Chrome Apps". You can see the Chrome developers making the decision to use the ~/Applications folder here. If you have installed any Chrome Apps, just uninstall them and delete the "Chrome Apps" folder and then Chrome shouldn't recreate the folder.
If you are using Chrome Canary, by default it installs shims for Gmail, Google Drive, Google Search and YouTube. But if you delete the "Chrome Canary Apps" folder it doesn't appear to recreate it.
There are other applications that install to that folder though. On my own machine Steam has installed shims for games and GitHub has chosen to install there app there instead of /Applications for some reason (I may have been prompted, I don't recall).
Like Tetsujin said though, having an Applications folder within your own user account isn't really anything to worry about.