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If the left frame is just for navigation, perhaps you could redo the pages to have the same links on the left of every content page, without the frame. Do it with CSS or tables. Make it fluid or not.
And welcome to WW.
They are useful on occasions but only on pages where SEO isn't an issue. I assume that the documents in question are not initially created as pages on the site so don't contain any in-built navigation when they come to you and you are unable or unwilling to edit them. The options there are a frame, either classic or iframe, or opening in a new window. Personally I prefer getting that sort of document in a new window but that is terribly confusing for a lot of people.
IMHO - avoid frames at all costs. If, as you mentioned, your navigation may get long, you could run into two problems: the frame will disappear below the window or visitors are going to have to scroll it thus having two scroll bars per page which I find to be a pain.
You would probably be better of with a standard navigation on the left or use a dynamic navigation on the left listing your articles by category and having each category expand/collapse or show/hide when selected. In this day and age, I believe more people are more comfortable with dynamic navigation than frames pages.
Marshall