Is there a way to open files stored in a document library in SharePoint 2013 in their native applications that aren't office files? For example, I am using SharePoint 2013 to store quickbooks files in a document library. I would like to be able to click on the document and have it open up in quickbooks. After doing some research on the web, there was nothing on the topic.
To Open files directly, you can look at the SPWebApplication.AllowedInlineDownloadedMimeTypes and BrowserFileHandling properties explained in detail here; there are security implications to changing these properties.
For an automatic check in/check out type behavior without saving locally, it is possible, but it is not easy, and involves changing the DocIcon.xml file on the server and deploying an ActiveX control to all client machines. See Open a BizAgi (or any 'unknown' documenttype) directly without saving
Note that Adobe Acrobat/Reader X and later support this with the DocIcon.xml change (the required control is included with their software); there may or may not be other non-Office products that do so.