Here's how to find those that are in your apps list but not in the extensions list:
Go here using the File Manager: ~/.config/google-chrome/Default/Extensions/
Click on the Find icon and choose the "Content" tab (assuming you have Dolphin. If not, you want to search in that directory for text in a file). Type in the name of your app. Then right click on the manifest.json file and choose "Open path in new tab." Find the big string of letters and numbers in the path at the top of the list pane - this is the app ID. Right click on the path and select copy. Then paste it in the text editor and copy the long ID number only to replace [AppID].
Sometimes, apps like GMail appear in many extensions so you may have to just go through each manifest.json listed to find the actual GMail app. First, it will be in a manfest.json file. second it will contain the gmail URL. That's how you know which one to use.
TIP: If you know the URL, use that for the search instead of the name to narrow it down. For example, I easily found GMail by searching for "mail.google.com".
Also, these IDs are the same no matter what machine you load chrome in as it's dependent on your login. If you change the login or remove and readd, then the ID will change. So it might be a good idea to keep a text file of these IDs so if you have to reinstall, you have the command lines ready.
HP Pavilion g7 2010nr 64-bit laptop running Linux Mint 14 KDE as the only OS.