http://www.idealware.org/blog/2009/07/why-sharepoint-scares-me.html
This is an excellent article which picks up on many of my current concerns having worked with a MOSS 2007 implementation for nearly two years. This is a Microsoft product, and of course IT departments of larger sized organisations will make the Microsoft choice precisely because of the integration benefits.
I'd say that to get the best out of a MOSS 2007 implementation, then all users should at least be us ing Office 2007 in tandem to make the best of the document management facilities and encourage collaborative working.