However, this does not always do what some people expect. CRM has 2 distinct concepts of a 'Default Organisation', and only one of them can be set using Deployment Manager. The 'Default Organisation' that you set in Deployment is a system-wide setting whose primary use is to define which organisation database is used by code that accesses CRM 4.0 through the CRM 3.0 web services (CRM 3.0 did not support multiple organisations, so the web services had no way to specify the organisation to connect to).
The other type of 'Default Organisation' applies to users. Each user has a Default Organisation, which is the organisation that they are connected to if browsing to a Url that does not contain the organisation name. For example, if a user browses to http://crm/Excitation/loader.aspx, then the user will necessarily be taken to the Excitation organisation, but if they browse to http://crm/loader.aspx, they will be taken to their default organisation, which has no relationship to the 'Default Organisation' that is set in Deployment Manager. Each user's default organisation will be the first organisation in which their CRM user record was created.
One issue that can arise is if a user connects using a Url that does not contain the organisation name, and either their default organisation has been disabled, or their user account in their default organisation has been disabled. In this scenario, the user would receive either the error 'The specified organization is disabled' or 'The specified user is either disabled or is not a member of any business unit'. The simplest solution would be to specify an appropriate organisation name in the Url; however if this is not possible, the rest of this post describes an unsupported alternative.
Unfortunately, none of the MSCRM tools will display a user's default organisation, nor is there a supported way to change this (though there is an unsupported way - see below). All the information is stored in the MSCRM_Config database, in the SystemUser, Organization and SystemUserOrganizations tables. The following output shows some of the relevant data from these tables:
The DefaultOrganizationId field in SystemUser defines each user's default organisation, and this can be joined to the Id field in the Organization table.
The fields that define the user are a little more complex: The Id field in SystemUser is unique to each CRM user. You can join the SystemUser table to the SystemUserOrganizations table using the SystemUser.Id and the SystemUserOrganizations.UserId fields. The CrmUserId field in SystemUserOrganizations can be joined to the systemuserid field in the systemuserbase table in each CRM organisation database. Note that the same user will have a different systemuserid in each organisation database. The following query illustrates these joins, taking the user's name from one of the organisation databases (it's not stored in MSCRM_Config):
select o.UniqueName, u.FullName
from Organization o
join SystemUser su on o.Id = su.DefaultOrganizationId
join SystemUserOrganizations suo on su.Id = suo.UserId
join Excitation_MSCRM..systemuser u on suo.CrmUserId = u.systemuserid
So, that's how it fits together. As this is all SQL data, it is not difficult to modify this, but be aware that to do so is completely unsupported, and could break your CRM implementation. If you were to make any changes, make sure you backup the relevant databases (especially MSCRM_Config) before you do so.
If you did want to change a user's default organisation, please heed the warning in the preceding paragraph and backup the MSCRM_Config database. The following SQL update statement will change the default organisation of a given user, based on their systemuserid in one organisation database. The reason for writing the query this way is to ensure that a user's default organisation can only be set to an organisation that they exist in, and this query should only ever modify one record. If it modifies 0 records, then check the @systemuserid value, and if it modifies more than one record then your MSCRM_Config database is probably corrupt, and you should reinstall CRM and reimport your organisation databases (I was serious about my warnings).
declare @systemuserid uniqueidentifier
set @systemuserid = '25E1DC1D-BEC2-449B-AAD8-4A6309122AE1' -- replace this
set DefaultOrganizationId = suo.OrganizationId
from SystemUserOrganizations suo
where suo.UserId = SystemUser.Id
and suo.CrmUserId = @systemuserid
One final point; CRM caches some of the data in MSCRM_Config, so you'd need to recycle the CRM application pool to sure any changes have taken effect.