So before we start, my problem was that my default $HOME_NET wasn't anywhere near broad enough, because of the configuration of my network. My network is fully NATed and includes all RFC1918 addresses, so since those RFC1918 hosts that are on non locally-attached networks are creating the traffic I want to inspect, and the default $HOME_NET is just locally attached networks, I did the following. If this isn't your problem, this won't help you, but here we go:
I went to Firewall - Aliases and made an alias called InternalIPs that contained the RFC1918's: 172.16.0.0/12, 10.0.0.0/8, 192.168.0.0/16 I went to Services - Snort - Pass Lists tab and created a new pass list , checked off all the auto-generated IP Addresses, and added my InternalIPs alias by name in the "Assigned Alias" field I then went to the Snort Interfaces Tab (under Services - Snort still) and under general settings for the relevant interface (LAN in my case), in "Home Net" under "Choose the Networks Snort Should Inspect and Whitelist" I chose the pass list I created in step 2, and also clicked "View List" and verified that all the networks I wanted to inspect traffic from were included. Save and then go back to Snort interfaces, stop and then start snort and see if stuff starts showing up.Of course also check the normal stuff - both Sourcefire OpenAppID Detectors options checked off in Global Settings, up-to-date AppID signatures in the Updates tab, you've got the right rulesets selected in the <Interface Name> Categories tab, and you've got both options under Application ID in the <Interface name> Preprocs tab checked off.
Hope this helps!