Confluence vs. Mediawiki

Paid support to fix problems in the core
Large paid team of developers continuing to develop system
Real wysiwyg editor
Draft saving
Plugins advantages
- Can be shipped as a compiled jar package
- Confluence plugin repository makes them easy to install for any developer
  - Plugins can easily be bundled and installed without any skill beyond handling ordinary web administration interface
- Wide variety of plugins types: New UI tabs, user macros producing HTML or wiki markup, event listeners, themes
Ships with several themes.
Third party sells an advanced theme add-in package
Atlassian claims Confluence is in use by 1800 companies
Confluence runs with a wide number of database packages
Permissions structure for spaces, and individual pages.
Supports blogging (news), in addition to wiki style content
Stores revisions of attachments
Has RPC API for wiki manipulation
Can allow automatic creation of new wiki spaces

Full source freely available
Wikifarm documented as available through having multiple config files, and to source to look at the request URI to select one of the config files - (Note: This is also a con, in that it is a roll your own solution.)
Greater bulk number of extensions (similar to Confluence plugins)
Wikipedia interface is well known
Only requires PHP + database, could run on windows or linux

Wikifarm probably not available, out of the box, to run whole farm from same database
No easy control panel to create wikis within wiki farm (could be done as extra web screen, and maybe backend scripts to edit the source, or system developed to place all config file options in a database.)
Updates (extensions) to system require someone proficient in php
PHP is not compiled, overall performance is probably less than a compiled java application.

Bugs in wysiwyg editor (For example: Does not handle preserving links in a pasted outlook email, or shows pasted email ok in wysiwyg window, but switching to preview or saving causes a roundtrip through wiki markup converter, and destroys formatting.)
No access to source code for non-paying users
Recompiling java system probably beyond abilities of most users
Event listener plugins can not veto events (for example, quota violation)
Will not run on [MySQL] 5.0+, requires [MySQL] 4.1+. Workaround may be to use [PostgreSQL].

Relative ease of google spidering of every nook and cranny within the wiki. For example, Usemod wikis are 100% spiderable, (rendered pages, wiki edit pages, diff pages, search pages, etc., everthing except for adminstration authenticated pages.)
Unknown if Mediawiki (php based application) will run with a wide variety of databases
Unknown the extent of mediawiki permissions support
Unknown if there are many alternate themes to the wikipedia look for mediawiki.
Unknown if mediawiki can store attachment revisions

Sources for evaluation:

http://www.atlassian.com/software/confluence/ - Confluence Wiki
http://www.wikia.com - (Almost) Wikifarm running on Mediawiki software - Does not allow automatic creation of new wiki spaces
http://www.mediawiki.org - Mediawiki software