Right now I'm trying to get Atlassian's basic JQL standalone gadget template working with my Confluence install (found here: https://developer.atlassian.com/display/JIRADEV/Writing+a+JQL+Standalone+Gadget). It renders just fine when I bring up the preview window, but it seems that the gadget kicks me out of my Confluence session as soon as it renders. This makes it impossible to place onto the page, and of course, impossible to use. Right now I have both OAuth and Atlassian Application links set up between my instances, what could possibly be causing this behavior?
Do you have your JIRA and Confluence instances on the same hostname but on different ports? To get the Application Links to function properly, you will want your JIRA and Confluence on two separate hostnames. Trying to use http://localhost:8080 for JIRA and http://localhost:8090 for Confluence is asking for trouble, especially for things like cookies and OAuth.
You don't need to move the servers at all, but you do need to set up different hostnames. For example, edit /etc/hosts to add "127.0.0.1 conftest jiratest" and then access them as http://jiratest:8080 and http://conftest:8090.
Once you've made those changes, make sure that you go into each application and reconfigure the base URL in the admin console according to whatever it is that you decided above, then delete and recreate the application links, delete and recreate the external gadget feed, and try again.
You may also want to turn on the Trusted Application feature in both the incoming and outgoing authorization for the application link (scroll down when you are configuring it—some parts of that dialog may not be visible above the fold). (Though maybe this is what you meant by "Atlassian Application links"?)