I'm using Google Chrome to set up site-specific browsers for Gmail, Google Reader, and such, so that I can use them like desktop applications. I've pretty much gotten it to work, except that external links open in a new Chrome window instead of my preferred browser, Firefox. Even if Chrome was my preferred browser, this still wouldn't work right, because the links open in the same instance of chrome as the site-specific browser (instead of my "normal" non-app Chrome). I want these site-specific browsers to work like desktop apps (e.g. Thunderbird) and open links in my preferred browser. Is there any way to do this?
No, even though you are making "applications shortcut" it is still using Chrome browser. Thus any link open in the "application shortcut" will be open by the corresponding application. Unless there is an extension, which I checked. You can drag the link to firefox and that should open it too.