In order to move objects from one domain to the other you can utilize the Active Directory Migration Tool. A temporary trust betwen the two forests/domains will need to be established in preparation. Once all of the objects are moved you can then remove the trust. In your case you can also simply use the ADDUSERS from the Windows 2000 Resource Kit or the LDIFDE tool.
For moving user mailboxed from the Exchange 5.5 to the Exchange 2003 server, you will want to use the Exchange 2003 version of a tool called EXMERGE. EXMERGE will allow you to export the user mailboxes as PST files and them import them. Alternatively, you can use a one step process to migrate them straight from old to new Exchange systems.