A clear downside to (an unmodified) dokuwiki is how it handles hierarchies of pages - you either have to manually move the files within the filesystem or install the PageMove plugin. (See http://www.dokuwiki.org/namespaces for more details.)
In Confluence, the page name is in the URL, and it's parent page is part of the URL path. In other words:
Also, the plugin management from Atlassian is better tied into the management interface
from a sysadmin POV
Dokuwiki has a low backup, system and maintenance footprint compared to Confluence. It's all in one directory so you can tar it up as a backup since there is no database connection to deal with.
While there are dependencies on PHP, you don't have to deal with installing Sun Java – something Confluence must run on, and isn't typically setup or available by default in package managers.
Memory-wise, Confluence requires 2GB at least. That works out to $80/month for a Linode VPS instance versus cheap shared hosting at say, Dreamhost.
the verdict? or, why sp00nfeeder uses dokuwiki
As usual, the correct answer is it will depend on the “situation” – or what the requirements are. Since I have an existing account on Dreamhost, I might as well make better use of what I'm paying for. Also, it's an excuse to go back to the original wiki I had started using versus Confluence, which I use as my personal knowledge base.