We have been running Sharepoint for a few years to support teams and smaller projects.
The biggest issue we have run into is migration from one machine to another. We had to retire the initial machine it was running on - and there is no good way to migrate the data between systems because Sharepoint creates and uses
local NTFS permissions that are machine specific .
This is a really large problem long-term - but we are now hoping that someone will come up with a way to help us maintain / migrate the data from the sharepoint before we have to retire the new hardware
Other issues are a lack of documentation and a backend DB structure that does not make a lot of sense / is not documented / difficult to read & write to.
We continue to use it for some things, but if you are going to base critical company docs on a web tool, I suggest first at least looking at some other options like Plone (
http://plone.org/ ) (Free Plone hosting
http://www.objectis.org/english ) or
Mambo.
We are looking to go in this direction ourselves. Good luck