Let's not get too bogged down in how all the searches are going to go, just yet. Even just rudimentary searching of notebooks is leaps and bounds beyond the current state of things.
Harvey's much more comfortable with LaTeX instead of WYSIWYG. I'm not sure how wide-spread this is... or how it will really work with pulling stuff in from a variety of sources.
Phases:
Formulation
Finding references
Keeping a bibliography of the things you browsed
Keeping annotations of the things you browsed
Proposing
Preparing a proposal
Experimenting
Finding algorithms
Writing algorithms
Running algorithms
Reporting
What if the notebooks were supported in multiple formats vs. something like Scientific Workplace?
How much structure do we need in a notebook? The notebook is a smart container. One of the things it contains is scientist's journal entries... those could be in LaTeX or Word or PDF or whatever you wanted.
Argument for a very web-ish interface so you can use it from anywhere.
Tangent: Notebook in a subversion or CVS tree? Put some thought into scoping of comments. Easy export for when someone wants to package up their data and go. It could be easy to merge together things.
need to keep track of meta-data for items
need to keep track of environment needed for algorithms
WebDAV is a good start
Notebook can watch a Folder... or you can something drag and drop...