Get it wrong, and you have dozens of re-work to do, especially if you've already designed and deployed the site with not much proper planning. Get it right and you'll be a celebrated SharePoint goody!.
I've come across a number of scenarios where sites are not planned properly in SharePoint, including the Hierarchial structure of team sites. Developers are called in just to build sites without a proper understanding or knowledge of what the long term purposes of a site will be.
For instance, a lovely guy I knew was asked to build an Intranet site with various pages, only to be told afterwards that BDC was needed on the site and page so that a third party data intensive application could be used for data mining purposes. It was no surprise when everyone pointed their fingers at the poor developer. Well, it wasn't his fault as a developer, but someone should have planned this properly (or maybe he should have been a bit more dilligent. Anyway, enough of the waffle. My suggestions are as follows:
- When planning for sites and pages, the strategy for organising web applications and site collections should usually follow "Intent" and "Function" i.e. this site / page will be used for such and such purpose and will have the following capabilities
- If you have created a web application for a specific project or purpose (for example the data intensive BDC application mentioned earlier) then create only the site collection you require to fulfill that purpose using that web application. Don't then lumber other site collections onto that web application, otherwise your could be faced with potential performance issues.
- If you have a more involved set of tasks, projects or sites to create, then create a web application and then whatever number and type of site collections within that web application, but don't then create data intensive applications on that web application.
- For manageability purposes, I would recommend 1 web application per BDC application.