Migrate between to Exhange 2003 servers

If both servers are in the same domain and both servers are Exchange 2000/2003, then you don't need the migration wizard at all.  Just right-click on the mailbox in the ESM and click Exchange Tasks then select Move, select to move it to the new server, and you're done.  You can select multiple mailboxes at one time and perform the Exchange tasks on all of them at one.

P.S. If they aren't in the same domain, then you must have Active Directory and DNS set up on the new domain before you can do anything else.  Then, you have to migrate your user accounts first before you can migrate the Exchange mailboxes.

I have tried the EMS way but it give the same result. I can't choose the new server in the drop down menu.

They are both 2003 servers but are set up as first servers in a new domain. So they are in different domains.

What must I set up in DNS?

If they're in separate domains, you can't do a direct migration.  The best way to do it in this case is to migrate your users, which you can do using the AD Migration Tool.  Then, create new, empty mailboxes for the users and use Exmerge to move the contents of their mailboxes from the old domain to the new one.

Another thought - if you're talking about large domains with 100's of users or more, you should look at 3rd party migration tools.  One company I know of that has such migration tools is Quest Software -www.quest.com.

The migration wizard is for going between domains.
Are you going across domains? It isn't clear from your question.

If you are not going across domains and are simply going to a new server then you need to do a swing migration. http://www.amset.info/exchange/migration.asp

Simon.

When I try to ExMerge it only succeeds on tree out of six mailboxes. The log shows the following:

ExMerge.log
****************************************************************
Microsoft Exchange Mailbox Merge Program, v6.5.7529.0
Start Logging:March 23, 2007   08:51:34
****************************************************************
[08:51:34] Logging Level: None
[08:51:34] Reading settings from file 'C:\Program Files\Exchsrvr\bin\EXMERGE.INI'.
[08:51:34] Reading list of subjects for messages to be selected from file ''
[08:51:34] Reading list of attachment names for messages to be selected from file ''
[08:51:34] List of folders to be ignored has been read. 0 folders in the list.
[08:51:34] Current machine locale ID is 0x409
[08:51:34] Operating System Version 5.2 (Build 3790)
[08:51:47] Accessing Domain Controller 'BRAIN'
[08:51:48] 'BRAIN' is running Exchange Server 2000 or later
[08:51:54] Mailbox '/o=Katzmann Consulting Org/ou=First Administrative Group/cn=Configuration/cn=Servers/cn=BRAIN/cn=Microsoft System Attendant' will be ignored as its DN contains strings in the ignore list
[08:51:54] Mailbox '/o=Katzmann Consulting Org/ou=First Administrative Group/cn=Configuration/cn=Connections/cn=SMTP (BRAIN)/cn={23A8504B-1CB2-4378-ADCC-70BA69939217}' will be ignored as its DN contains strings in the ignore list
[08:51:54] Mailbox '/o=Katzmann Consulting Org/ou=First Administrative Group/cn=Recipients/cn=SystemMailbox{23A8504B-1CB2-4378-ADCC-70BA69939217}' will be ignored as its DN contains strings in the ignore list
[08:51:54] Found 11 mailbox(es) homed on database 'FIRST STORAGE GROUP/MAILBOX STORE (BRAIN)'.
[08:51:54] Ignored 3 mailbox(es) homed on database 'FIRST STORAGE GROUP/MAILBOX STORE (BRAIN)'.
[08:51:54] Found 11 mailbox(es) homed on the specified databases.
[08:51:54] Ignored 3 mailbox(es) homed on the specified databases.
[08:52:57] Using attribute 'PR_MESSAGE_DELIVERY_TIME' for date operations.
[08:52:57] Merging data into target store. The program will copy only those messages that do not exist in the target store.
[08:52:57] Associated folder data will NOT be copied to the target store.
[08:52:57] Using 'English (US)' (0x409) as the default locale (Code page 1252)
[08:52:57] All mailboxes will be processed, regardless of locale
[08:52:57] Using last logon locale for all mailboxes, if possible
[08:52:57] (Thread0)Copying data from mailbox 'Cathrine Katzmann' ('CAT') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\CAT.PST'.
[08:52:57] (Thread1)Copying data from mailbox 'Daniel Katzmann' ('DK') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\DK.PST'.
[08:52:58] (Thread0)Errors encountered. Copy process aborted for mailbox 'Cathrine Katzmann' ('CAT').
[08:52:58] For more information, please refer to file ExMerge-(Thread0).LOG
[08:52:58] (Thread0)Copying data from mailbox 'Christian Katzmann' ('CKA') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\CKA.PST'.
[08:52:58] (Thread1)Errors encountered. Copy process aborted for mailbox 'Daniel Katzmann' ('DK').
[08:52:58] For more information, please refer to file ExMerge-(Thread1).LOG
[08:52:59] (Thread1)Copying data from mailbox 'Kasper Katzmann' ('KK') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\KK.PST'.
[08:52:59] (Thread0)Errors encountered. Copy process aborted for mailbox 'Christian Katzmann' ('CKA').
[08:52:59] For more information, please refer to file ExMerge-(Thread0).LOG
[08:52:59] (Thread0)Copying data from mailbox 'Claus Katzmann' ('CK') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\CK.PST'.
[08:53:21] (Thread0)Successfully completed copying mailbox 'Claus Katzmann' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\CK.PST'.
[08:57:52] (Thread1)Successfully completed copying mailbox 'Kasper Katzmann' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\KK.PST'.
[08:57:57] (Thread1)Copying data from mailbox 'Katja Katzmann' ('KATJA') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\KATJA.PST'.
[08:59:03] (Thread1)Successfully completed copying mailbox 'Katja Katzmann' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\KATJA.PST'.
[08:59:06] Number of items copied from the source store for all mailboxes processed: 4023
[08:59:06] Total number of folders processed in the source store: 58
[08:59:06] 3 mailboxes successfully processed. 3 mailboxes were not successfully processed. 0 non-fatal errors encountered.
[08:59:06] Process completion time:  0:00:06:08
---------------------------------------

ExMerge-(Thread0)
****************************************************************
Microsoft Exchange Mailbox Merge Program, v6.5.7529.0
Start Logging:March 23, 2007   08:52:57
****************************************************************
[08:52:57] Logging Level: None
[08:52:57] Initializing worker thread (Thread0)
[08:52:57] (Thread0) processing the range of mailboxes from 'Cathrine Katzmann' to 'Claus Katzmann' (index 0 to 2)
[08:52:57] Copying data from mailbox 'Cathrine Katzmann' ('CAT') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\CAT.PST'.
[08:52:58] Error opening message store (MSEMS). Verify that the Microsoft Exchange Information Store service is running and that you have the correct permissions to log on. (0x8004011d)
[08:52:58] Errors encountered. Copy process aborted for mailbox 'Cathrine Katzmann' ('CAT').
[08:52:58] Copying data from mailbox 'Christian Katzmann' ('CKA') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\CKA.PST'.
[08:52:59] Error opening message store (MSEMS). Verify that the Microsoft Exchange Information Store service is running and that you have the correct permissions to log on. (0x8004011d)
[08:52:59] Errors encountered. Copy process aborted for mailbox 'Christian Katzmann' ('CKA').
[08:52:59] Copying data from mailbox 'Claus Katzmann' ('CK') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\CK.PST'.
[08:53:21] Number of messages processed for mailbox 'Claus Katzmann': 38
[08:53:21] Number of folders processed for mailbox 'Claus Katzmann': 12
[08:53:21] Successfully completed copying mailbox 'Claus Katzmann' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\CK.PST'.
--------------------------------

ExMerge-(Thread1).log
****************************************************************
Microsoft Exchange Mailbox Merge Program, v6.5.7529.0
Start Logging:March 23, 2007   08:52:57
****************************************************************
[08:52:57] Logging Level: None
[08:52:57] Initializing worker thread (Thread1)
[08:52:57] (Thread1) processing the range of mailboxes from 'Daniel Katzmann' to 'Katja Katzmann' (index 3 to 5)
[08:52:57] Copying data from mailbox 'Daniel Katzmann' ('DK') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\DK.PST'.
[08:52:58] Error opening message store (MSEMS). Verify that the Microsoft Exchange Information Store service is running and that you have the correct permissions to log on. (0x8004011d)
[08:52:58] Errors encountered. Copy process aborted for mailbox 'Daniel Katzmann' ('DK').
[08:52:59] Copying data from mailbox 'Kasper Katzmann' ('KK') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\KK.PST'.
[08:57:52] Number of messages processed for mailbox 'Kasper Katzmann': 3496
[08:57:52] Number of folders processed for mailbox 'Kasper Katzmann': 29
[08:57:52] Successfully completed copying mailbox 'Kasper Katzmann' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\KK.PST'.
[08:57:57] Copying data from mailbox 'Katja Katzmann' ('KATJA') on Server 'BRAIN' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\KATJA.PST'.
[08:59:03] Number of messages processed for mailbox 'Katja Katzmann': 489
[08:59:03] Number of folders processed for mailbox 'Katja Katzmann': 17
[08:59:03] Successfully completed copying mailbox 'Katja Katzmann' to file 'C:\DOCUMENTS AND SETTINGS\KK\DESKTOP\MIGR\KATJA.PST'.
-------------------------------------

It doesn't make any sense to me.

The account that you're using to run Exmerge probably does not have Full permissions to the mailboxes that are failing.  Go to your original Exchange server and make sure the account has FULL Access to all of the mailboxes.

Are you crossing domains?
If you are not, then you don't have to exmerge.
You simply move the mailboxes.

Simon.

Yes I'm crossing domains, but as hypercat mentioned I don't have the right permissions. So I decided to join the ExMerge group, but it doesn't exist on the server.

Any ideas on how to implement the ExMErge group?

I can't thank you enough. It worked fantastic.
But if you drop by, I buy you a beer :-)

Kasper
Smørum, Denmark

Pity I don't drink really...

Simon.