The quickest way to fail from a user perspective is to not train your users how to build a good site taxonomy in collaboration with IT.  Remember that you want to build your taxonomy wide not deep.  Use the 6 P's and you will have a true collaboration site that will last.  Failure to do this up front will cause you to have to spend a lot of time exporting & importing your sites to get it right.

Planning worksheets for Office SharePoint Server 2007
URL: http://technet2.microsoft.com/Office/en-us/library/49cf7edd-14ee-445b-8ab0-1d1339f2435f1033.mspx

Plan Web site structure and publishing (Office SharePoint Server)
URL: http://technet2.microsoft.com/Office/en-us/library/6a4b0ec4-8802-40f9-87ac-6a6691b544a41033.mspx

Plan Web site structure and publishing (Windows SharePoint Services)
URL: http://technet2.microsoft.com/windowsserver/WSS/en/library/aa456629-8de8-4328-873b-2e2db96714011033.mspx

Plan site navigation (Windows SharePoint Services)
URL: http://technet2.microsoft.com/windowsserver/WSS/en/library/a7e52934-30ff-455d-bfcd-52a3e0ff170a1033.mspx

Logical architecture components
URL: http://technet2.microsoft.com/Office/en-us/library/aaed3a01-f4dc-4353-abda-0beced2080b61033.mspx

Design Records Center architecture
URL: http://technet2.microsoft.com/Office/en-us/library/f82c58ba-6d25-406d-835e-aa00acd5b76d1033.mspx

Once you have done this you need to plan site navigation

UNDERSTANDING SITE COLLECTIONS AND SITES

By default, all content for a Web application is stored in one content database. You can separate content into multiple content databases at the site collection level. A content database can include one or more site collections. A single site collection cannot span multiple databases. Backing up and restoring sites takes place at the content database level.

Site collections will allow the IT department freedom to maintain just application itself without the worry of security or content hierarchy maintenance. The following is a list of what an individual site collection offers.

For the Users:

  • Dedicated Recycle bins
  • Dedicated usage Reports
  • Distributed administration (site collection administrators)
  • Dedicated search scopes, keywords, and best-bets
  • Custom feature deployments
  • Dedicated language translation maintenance
  • Dedicated galleries for web parts, master pages, content types, site columns, site templates, and list templates
  • Dedicated shared libraries, such as site collection images and site collection styles
  • Dedicated real estate (Self Containment)

For the IT Administrators:

  • Site quota templates
  • Distributed administration
  • Site locking
  • Database maintenance options
  • Backup / Restore abilities
  • Content Deployments
  • InfoPath forms services global template targeting

Top Level Sites - Usually created by department, project, etc...

Resources that will help you plan your taxonomy

Decide whether to use individual site collections or subsites within one site collection

You must decide whether to create your sites as top-level Web sites in separate site collections, or as subsites within the same site collection. This decision is based on how much the sites have in common with each other, whether you want to be able to manage them individually, and whether you want them to share elements, such as navigation or search.

Within a site collection, all sites can use the same:

Navigation bars (top link bar and breadcrumb navigation)

Content types

Workflows

Security groups

Lookup fields across lists

Search scope

Feature set

Choose top-level Web sites in separate site collections when you:

Need separate security for different sites.

Note:

Although you can have unique permissions for a subsite, at times you might want to be sure that there are no users and permissions in common between two sites. In those cases, you should use separate site collections.

Might need to move the site collection to a different database in the future.

Want to be able to back up or restore that site only.

Want to be able to scope a workflow to that site only.

Want to have a separate search scope for that site only.

Want to use quotas to separately manage the amount of space that each site takes up.

Want to decentralize your administration and have site collection administrators perform tasks, such as approving requests for access or confirming site use.

Choose subsites within the same site collection when you:

Want to share navigation between sites.

Want to have subsites inherit permissions from parent sites.

Want to share lists between sites.

Want to share design elements (such as themes or styles) between sites.

 

Zones represent different logical paths (URLs) of gaining access to the same Web application. Within each Web application, you can create up to five zones using one of the available zone names: Default, Intranet, Internet, Custom, or Extranet. Each zone is represented by a different Web site in IIS.

The Default zone is the zone that is first created when a Web application is created.

Capacity

You can create up to five zones within a Web application. A farm that hosts more than one Web application can support user requests from more than five different network zones. Typically, zones are coordinated across Web applications so that zones of the same name are configured for the same users.

Sharing and isolation

Zones provide a method of partitioning users by:

Authentication type   Each zone can be configured to use a different authentication provider, enabling you to share the same content across partner companies.

Network zone   Each zone can be configured to accommodate users entering from a different network zone, such as an extranet or the Internet.

Policy permissions   You can explicitly allow or deny read or write access to content per zone based on a user account or a group account.