Alas and alack, they were removed and all that exists in their place is a collection of sample code. They'll be making a comeback in Apex 4.2 where they will be 'prepacked' in the installation and ready to install. You can keep them vanilla, and perhaps get some support from Oracle for them (or maybe just an upgrade path), or you can unlock them and make your own customisations and enhancements.
These packaged productivity apps also got mentioned as part of the cloud.oracle.com offering. Assuming that does eventually materialize. Maybe its been waiting for Apex 4.2. (By the way, the EA is running on 11gR2 so there's no 12c hiding there.)
The only drawback is that the new packaged applications won't be available for anything earlier than 4.2. I guess it is possible for someone to unlock them and somehow achieve a backport to an earlier version, but I wouldn't count on it. Certainly don't expect that from Oracle.
Anyway, for a bit of nostalgia, I dug out one of those old packaged apps from my hard drive. The original Issue Tracker was developed for Apex 2.2 and is old enough to be attending school. The new one looks a lot more attractive. Since it caters for features such as uploading attachments, it looks much more like a usable application than a sample or demo.