I have upgraded recently to Exchange2010. Certain users are getting
NDR back when trying to email certain domains, ex: .gov. .net.
Sometimes my domain might get put on spam list. It doesn't happen to
everyone. Why is this?

The domain is not listed on a blacklist, but we keep getting these
individual instances of failure.

following domains:

illionios.gov
yahoo.com
amwater.com

ESMTP gave this error:
Transaction Failed Spam Message not queued.

A problem occurred during the delivery of this message to this e-mail
address. Try sending this message again. If the problem continues,
please contact your helpdesk.