I can't speak a whole lot to integrating OJS with another CMS. That depends on how far you want to go theme- and hook-wise, I suppose. OJS uses the Smarty template engine and css to style the whole thing, so with some work you should be able to get it to look like pretty much anything you want. OJS also has a plugin architecture which makes creating custom, non-core code easier, and 2.2 includes a 'block' architecture as well, somewhat similar to Drupal's block/module system. I know a couple of different groups who have built their own custom blocks for the sidebars etc., with whatever info they need in there. Aside from that you may want to worry about user authentication; there is an LDAP plugin, but I've never used it (I can get some advice from folks who have if you need it, however).
All that said, it depends on the level of integration you need. There are very easy ways to add links etc. to the navigation bars if that's all you need.
Regarding the other items you are looking for:
* There's a fair bit of info on BibTeX on the forum: search.php?st=0&sk=t&sd=d&keywords=bibtex
* OJS supports uploading related files with articles during the submission process (called Supplementary Files; they can be pretty much anything);
* OJS has good support for HTML, PDF and PS galley files, but you can use many other types of file for you galley. Others have successfully experimented with using audio and video files for galleys (you can search the forum for specific threads);
* We may look at tagging as a feature down the road.
If you have any further questions, please let us know. I would suggest taking a look at the OJS development forum as well, to get an idea on what other folks are doing. Also, you may want to take a look at some of our bits of documentation, especially OJS in an Hour for a complete overview of OJS features, and the OJS Technical Reference. The Technical Reference is a couple of revisions out of date, but we'll be updating it shortly.
Development Forum: viewforum.php?f=9
OJS Documentation: http://pkp.sfu.ca/ojs_documentation