To the having to authenticate every time issue. What you can do to
stop this problem is have all users add the url of the your portal
to there local intranet or trusted sites. The easiest way to do
this is push it using active directy policy. Once thhey have this
they should not get prompted every time.

As for the list of users in the check in/check out on the left. If
some of the users are showing up as there prefferred name (FirstName
LastName) and some are showing up as usernames (DomainName\UserName)
read this article I wrote and it should solve your problem.
It will also help if your users have problems receiving portal
alerts as well.

sharepointinsight.com/.../Post.aspx?ID=11

That's EXACTLY the problem I've been having!

For some reason the user base has to re-authenticate to the domain when
they are attempting to do something with a file. Our issue  is not with
the web browser asking us for credentials, but being prompted for a
logon anytime a physical document is involved in a sharepoint
transaction.

Any thoughts on that one?

(Oh, and the SPS2003 sites are Trusted...)

"To the having to authenticate every time issue. What you can do to
stop this problem is have all users add the url of the your portal
to there local intranet or trusted sites. The easiest way to do
this is push it using active directy policy. Once thhey have this
they should not get prompted every time."

Unless you have SSO set up, there is no way for the client application
(native document application) to authenticate to SharePoint when challenged
for credentials. If you keep the client application open, you can then
traverse documents without being challenged. Once you close it and request
another document from SharePoint, the user will get prompted again. This is
by far the biggest complaint of non-technical users in v2.

Do you know if this is addressed in any way with the latest version?

I'm not sure as I've just set up my MOSS environment. It appears to support
SSO out of the box, but that's all I know for sure.

You might want to read http://support.microsoft.com/kb/871155/en-us

None of our users are prompted for this UNLESS they are outside of
the firewall/VPN. If they VPN in from then they will stop getting
prompted. The adding of trusted sites will help in the HTPP request
realm in the browser. We recommend all users use a VPN connection
to access the portal when working outside of the office. Beyond
this I don't have a solution

The article that is referenced below should be like this by
default. If a user is on there home machine not authenticated
through the domain the integrated security is not going to help.

Single sign is one solution that be implemented but its a PAIN IN
THE REAR to setup if you don't know SSO. You can use SSO on SPS
2003 as well.