This seems to come back to me all the time, the question how to build a perfect site structure to use inside a company. And my answer? Indeed, perfect would be perfect!
What I mean is that it all depends on your organization. Things like big or small, projects or departments etc.
Projects or departments
In the projects that I was involved in it always came to these two. Are we a company that uses the project approach or do we have a more static organization with departments that support each other and a product we deliver.
The size is also important. The bigger the site structure the bigger the chance that you need more site-collections. Webapplications is not your concern to decide on, let the IT guys decide that. Be aware that you can lose some out of the box functionality when using different web applications. It is wise to ask your IT department to draw a list of things that don't work between web applications (hey, you are only the end user remember).
I would always go for site-collections, for departments and for projects. For projects below departments I would create a site inside a site-collection. However, I would create it below the department that is the owner of the project. If it is a huge project you could define it as a site-collection too. Lots of choices to make.
Meeting workspaces
And what about meeting workspaces? Well, you can have different kind of meetings too. Some are probably project related and some are not. Always use common sense when deciding this. If meetings are setup for projects try to create a meeting space inside a project site. This way you always use the logical tree that SharePoint uses. For other kind of meetings in case of the project approach you could create separate site-collections. In case of the department approach you could put them below the department.
Security
Now we're talking. Yes, this can be a pain in the bottom. I al depends how you have set it all up (AD). Individual rights are a big problem. Also with search I believe (need to ask Daniel that). In some organizations this is a incredible mess. There is no straight answer.
Folders or tags/META information
Mmm.., now you have me. Microsoft always promotes using tags or META information but, there are limitations in how many documents and documents per folder so that makes it more difficult. One thing is for sure, never have views that return thousands of items (that hurts). Luckily in 2007 the current state of a view is saved (poor old 2003 users) and you don't have to collapse the whole tree again to get to your document.
I would say, forget your whole idea of folders and files and use search instead. I know, easy to say. I myself have this habit of using folders to organize everything. We have been trained and brainwashed for years to use folders. And even worse, before the computers we already used folders stored in a file cabinet. Aarghh...
There will always be a smart guy in your organization saying, "I'm used to search because I use Google so for me it is so normal". Well, he probably forgets that he always clicks 500 times next to get to the right document :-)
Luckily SharePoint search is good and you probably have less documents. Chance of having a direct hit on the stuff you need is much bigger.
So my idea, go for search!