I've been looking at this today. I'm using Deki at the moment and I was trying the Confluence standalone .exe eval install.
I like deki, the desktop connector is very useful and the office tools looks interesting as well.
Linking a single email to a single Page from Outlook is good and bad - good because the deki mechanism goods straight forward and easy for the user, plus the content is movable after the fact. Bad because it doesn't provide linking between emails in the Deki. It's a shame that the msgid or subject is not made into a tag when the email is import.
Confluence system is good for a bulk set of emails. Emails can be archived via POP or IMAP into a Space. However, doesn't seem to be a way to move emails or link them to pages.
They both have a good webdav server.
Confluence has a very nice mechanism for editing a page directly via Word or OpenOffice over webdav. Works well. This makes up for the fact that Deki has a much better Wysiwig editor. Deki's editor can handle pastes with images from webpages, the Confluence editor drops the images. Although Confluence does seem strip that crap from "pasted" content - whether this is good or bad depends on the purpose.
I think Deki have a better permissions model, although it still could be improved.
Finally, from my investigations today. One thing Confluence does much better than Deki at the moment is provide addon scripts. The Confluence Form Scaffold [1] is probably possible with Dekiscript, but it doesn't exist yet. This is a big shame, and one reason why I'd consider switching. Confluence is more along the lines of a Twiki application style wiki, with some extra tool functionality.
On the Deki side, the CRM integration looks very useful. Again this is probably something possible with Confluence, but is not avaliable.
I'm not sure about the price difference anymore as Deki removed the pricing from their website recently. Last time I checked though the price for standard Deki was very good.
At the end I'm not sure which is the best at the moment. I will probably stay with Deki as given the email archiving is not more useful than Deki's and the Word/OOo functionality not enough. the Form Scaffolding would be the only thing that might convince me. Their are some hints that Mindtouch have something like this, but I haven't seen any code yet.
If either wiki got an IMAP portal like OpsMailManager [2] for alfresco I'd probably jump on them. In fact given this major point that will be driving Sharepoint for Exchange archiving in the future I hope either does build something like this.
[1]
http://confluence.atlassian.com/disp...+Form+Scaffold
[2]
http://www.opsera.com/jsp/opsera_pro...ailmanager.jsp