We have replicated our base Ektron site over 100 times (different clients) and between copies on the web servers and putting sites in SVN, I have decided to pull out the scalpel and slim down the workarea.
Folders that I find take up the most space:
Has anyone done this and what have you cut?
The current version of ektron (v8.5) supports a true 3-tier architecture. This is relevant to your situation because it would allow you to have a single full Ektron installation on the middle-tier (application server), and have a very minimal configuration on the front-end (presentation server). The minimal configuration on the presentation server would not require you to have any workarea folder, nor would it require all of the DLLs in the bin folder. Ultimately it gives you great control over what you place on your front-end presentation server.
I have a webinar on this exact configuration coming out on 9/15/2011. It will cover installation, configuration, the developer experience, best practices, etc. If you're interested, keep an eye on this page http://www.ektron.com/Resources/Webinars/. If you visit this link after 9/15/2011, the webinar should be recorded, archived, and available on that page.