I'm having a horrible, and completely intermittent
problem.

I have one server, which acts as a domain controller, DNS
server, file server, VPN server, and lastly, a DHCP server.

When the server is booted fresh, everything works great,
everyone can access all websites (anything on the internet
their heart desires, including me). However, within a few
weeks of the server running, some DNS queries to web
sites, stop working. For example, no one could all of a
sudden log onto MSN messenger, or access YouTube. If
going to youtube by IP, all is good, but DNS was not
translating the name. Rebooting the server fixed the
problem.

However, this constantly rebooting is not practical, as the
RAM count is slow, and so is starting 2003 itself on this
server.

No event logs are ever triggered, all is good there.

So, what can cause the sudden and intermittent loss of
DNS query on some sites? The sites affected are totally
random too. This was the first time a service (MSN
Messenger), was affected by this problem.

Ok, temp workaround seems to have TWO DNS servers in my
DHCP scope. My DNS server, and the ISP DNS server.

Only problem is, when I do this, I can no longer access local resources, because the DNS server doesn't want to respond anymore. (it gives back that it can't find anything..)

One such site that won't forward no matter how many reboots, is: www.oratan.com

that site is causing hell on my DNS forwarding... please help!

Is there configured any dns server, e.g. the dns server of your ISP, in the forwarder tab of your DNS server, so that your dns server is responsible for the local name resolution and the ISPs dns server is responsable for the internet name resolution?
That doesn't mean, that every client directly connects to the ISPs dns server for name resolution. Your server is asking the ISPs dns for name resolution.

Simple: you should not be listing your isp's dns server in dhcp. It should only be listed in the forwarders tab [not to be confused with forward lookup zone]

Imagine the power if you knew how to internet search

I could have sworn I had the forwarder setup as my ISP.

Somehow the IP address to my ISP's DNS server disappeared
from the forwarders tab.

Added the IP there, and problem is all fixed.

I'll need to keep an eye on it.