Re the idea of storing notes seperately:
InfoQube's (IQ) notes are html and are stored seperately from the database file by default
The HTML pane displays content (web &/or notes) related to items
The HTML content can also be stored/saved as MHT (as html it cannot yet store images locally AFAIK)

Reading your first post Josh: I think IQ
could fit the bill
e.g. I can create links to files (or to other items, or to urls) in the Grid (left side in screenshot) & in the html pane
or
I can simply open e.g. a PDF file in the html pane and next time I click on the related item in the grid the pdf file show again - I
believe the files shown in the html pane can also be saved in a folder in same directory as the database file. (I work mostly with files linked to items in the grid myself)
I have Softmaker/Textmaker and I find the html pane opens doc files externally - I believe with Word installed it shows doc files within the programme
This would not be covered:
Ideally, each page would allow for thumbnail generation to get a quick glimpse of the pages in each "book" without opening them all them completely. Of similar function, or perhaps a substitute, is just displaying the associated icon of the program used to open each document so you know it's type.
and
I'm not sure what you mean by a "CHM file creation tool"
IQ is still in Beta:
Pros - very responsive developer
Cons being it has a learning curve cause the interface at times not yet so user-friendly, and also cause it's so flexible (- but having a fair idea what you want to do with it helps - you'd get a lot of help at it's forums too)