I will say it depends on your company size and content.

We have found that for organization  smaller than 2000 employees creating one portal  and area for each departments was the best solution. The configuration is easier and there is less to maintain. In addition using team site for collaboration further enhance the experience

For large organization and for scalability issue, you may want to consider creating many portals.

I am also facing this problem. In our organisation we
have 2000-3000 employees. Let me understand properly
for designing the portal. Shall i create  area or wss
or portal  site for each division. our each departement
come under 200 plus employees.

If i create portal site for each division, then
problem for publishing corporate news.

I am not able to find any document which can explain
deeply from microsoft website.

I will say you need both portal  areas and team site.

As a rule of thumb.

Portal areas  are used for content which is company/organization facing.
Like for each department public information about the department and
document/content related. Team Site will be used by each department. You
can think about having a root team site for each department with
sub-sites for each team/projects.

You need to prototype and find out what works best for your organization

In any case, I will recommend creating one portal site fo rthe entire
organization and areas for each departments for public content and team
sites for each departments/team/projects with root collection to make
easy to access/find

Let me know if you need additional help.

Look at Shared Services... will aggregate all the MySites, alerts, and search  into one central portal  that all portals  will share. Make sure you research it fully because once it's enabled, there's no going back.

The problem  you'll run into is navigation... the SharePoint portal navigation isn't "aware" of other portals. That's the issue we're having now... so replacing default SPS navigation with our own that will show  the other portals.

With respect to your issue, couldn’t you put all links  to child portals  in the site directory of your parent (main) portal? With Shared Services you got to have a parent, usually, a corporate portal  aggregating divisional (child) portals. You can then modify the home pages of child portals to have “Up to Main Portal” type links (normally associated with portal’s WSS sites) that allow users to navigate back from children to the parent. That’s one type of navigations for integrated portal setup - one that we are currently piloting

I could put the links  in the sites list, but frankly I don't think that's intuitive (nor does or group doing the planning of the site). The navigation needs to really show  things in the single  navigation... needs to be more intuitive than having to go somewhere to get stuff... single navigation... not "go here to find sites"... the left hand nav (and top as well) need to be context aware to show you where you are int he overall hierarchy.