I would start out by reading the microsoft windows 2000 domain migration cookbook. This should give you a good idea of what the best options are.
Once you are ready, check out the domain migration wizards that come with server 2003.
When our techs migrated some separate win4.0 domains into our win2k domain, the main stumbling block was name conflict between the OUs they had created for testing and the new domains with the same name. Other than that, things went smooth. We have retained the old domains until the new quarter just in case there are any unforseen issues when the students come back. After the new quarter, we plan on decommissioning all of the old independant domains.