I am banging my head against the wall here. I have basically a fresh install over server 08, TFS 2010 (don't get me started on TFS 2008), and WSS 3.0 which was packaged and installed with TFS. Unfortunately TFS is boned because WSS3.0 and WSS 3.0's Administrator Panel are unreachable. The app pools are running fine in IIS and previously, it would prompt for a username and password and then 404 (it is no longer doing so).
Has anyone ever experienced this? If so, what did you do to correct it / what should I look for? Thank you so much in advance!
Check your IIS logs. The 404 has a lot of subcategories.
It sounds like the handler may not be enabled, tho.
The Windows Event log might turn some details. I would also look at Sharepoint logs (under the 12 hive).
Can you connect to your DB server from your web server?
Have you setup the correct account permsisions? link
Are you sure the right version of ASP.Net is mapped to the website?
Are you trying to access from the WFE server?
There is a security feature in WS2003 SP1 and WS2008 which blocks requests coming from the machine hosting the application. Here is a link to a good blog post on the details of the problem and best practice for overcoming it http://harbar.net/archive/2009/07/02/disableloopbackcheck-amp-sharepoint-what-every-admin-and-developer-should-know.aspx
A hard problem to diagnose as you won't see anything useful in logs etc. because nothing is actually failing!!
Try re-running the SharePoint Products and Technologies Configuration Wizard to re-establish Centeral Administration. Once you get that up and running you can make whatever other configuration changes are needed to get the rest of SharePoint going.