Yes, I know this is about version 3.0, but yes not everybody uses 4.0 already. I see and hear that companies looking and research upgrade to the latest version, but often they have their custom applications which need further testing or redevelopment to make it compatible with 4.0.
The enterprise roll-out is bit different from regular roll-outs more users, more locations, international aspect etc. Most issues I am facing as consultant are architectural, network, product related issues.
The architectural issues are basically about providing the best server setup for providing all users a good technical performance and user experience, the latest is key issue for acceptance of your CRM application. And not forget the personal pc or laptop, an upgrade will do miracles :-)
The network issues are more divers it’s from internet connections, wiring in 19”rack, network availability, configuration of proxies, network routing, authentication/authorization (Kerberos) etc.
Often you will encounter network latency which can lead to slow experience at end user, loss of authentication/authorization (username/password dialogue boxes), time-outs etc
Some related knowledge base articles could be:
The product related issues are mostly result of the above mentioned issues, so related to architecture or network. Also to my surprise also common things like not comply to specifications of Microsoft Dynamics CRM an example is roaming profiles this is not supported in 3.0.
Also be careful with security roles if you reduce rights or disable them this could lead to issues in the user interface. See for example: http://support.microsoft.com/kb/930793/en-us
How you should identify your issues? The standard checks I use are check basic functionality open Outlook Client, Open site in Internet Explorer etc. Next step would be check all windows updates & crm updates (check: http://support.microsoft.com/kb/927751/en-us), check event viewer, the source for all your misery ;-)
And if you really want to have start sniffin the network, track the packages and run your server or client in debug mode, see http://support.microsoft.com/kb/907490/en-us
Hope this gives you some clues how to track issues within your project. More interesting tips just leave them in the comments.