I know that the documentation on using the WSPBuilder hasn't been fulfilling to say it nicely, but that's the way it is.
The good thing is that other people have been nice and done some work on this. This is what I have found so far (in random order), sorry if have forgot someone.
WSPBuilder - Walkthrough of the Visual Studio Add-in
WSS: Development - Quick Start with WSPBuilder
WSS Dev: WSPBuilder Templates
WSS Dev: HowTo debug a WebPart
Change the WSPBuilder DeploymentTarget to WebApplication
Intro to WSPBuilder
WSPBuilder Folder Structure
Developing SharePoint Solutions in Visual Studio
TFS Build and WSPBuilder
How to get TFS to automate your WSP builds with WSPBuilder
The WSPBuilser Manual
Creating a code-only webpart and deploying as a feature
Please comment with more links if you know one.