CiviCRM Community Forums (archive)

The answer to this depends on how the organization's staff will interact with the data. If the same staff members typically need to access data for the different types of organizations during the course of their work - then putting all the data in a single instance starts to sound like a good idea. However, you'll want to get a decent understanding of the constraints of the "Profile" functionality before going that direction.

For example, transactional info like Activities and Memberships - as well Relationship data - can not be exposed in Profile screens.

You should also explore whether using the built-in contact view and edit screens, and configuring the different sets of custom fields in tabs, is a usable approach. You could also look at creating a customized version of the built in contact view template which dynamically includes the appropriate custom fields depending on an organization type "tag" value.

On the other hand, if organization staff / work-flow is divided up by organization type - then separate instances might be the most straightforward. Consider configuring your installation so that the instances share a single codebase to make upgrades easier. Some folk are using the multiple-domain / single CiviCRM DB model as well - perhaps some of them will chime in here. :-)