I have done exactly the kind of technical manuals of which you speak, and I have always used InDesign (actually started on PM 6.5 and converted to ID 2.0). My FrameMaker experience is limited to playing with the trial version for a few hours. As far as I know, FrameMaker is no longer supported for the Mac platform, and many of its long documents features (footnotes, endnotes, etc.) are now part of IDCS3. Some other long document features have long been a part of InDesign (TOCs, indexes, etc). From one who has spent years creating long documents, InDesign lacks nothing for me. It has more long document support than I have ever needed. Some of my favorite features for use in manuals were tables, native PDF placement, shadows, nested styles, and the best character and paragraph styling EVER. Let me tell you, I did a happy dance around the office when nested styles came out! Same as for running table headers and alternating fills and strokes. Wow, that was a great day! And now IDCS3 has bought Teacup Software "Cell Styles" and "Table Styles" plugins, so those features are built in right out of the box. Very cool. I haven't done long docs in a couple of years, but I think I read that there was now support for figure numbers as well. Like, "please refer to figure 1.3 on page XX.", and when the figure gets moved, the page numer reference will get updated. That feature is not that exciting to the average designer doing brochures and business cards, but if you're working on a 1000 page document and have several thousand figures to keep track of, this is HUGE! I know FrameMaker has probably had these long document features for quite some time, but I like ID because its got a beautiful interface (when I used FrameMakers, it was very clunky) and is friendly toward making manuals beautiful in addition to functional. And I can use it on a mac.
ID is also highly scriptable and has support for XML documents.
I've never met another prepress person who had any FrameMaker experience, so converting to InDesign may be helpful to whoever their output provider is, as they could easily work on the native files if need be. Again, this may not matter, if they're just sending PDFs, and don't use every transparency effect under the sun. Technical manuals tend to be very predictable and rather boring visually, so that type of PDF might not need much (if any) prepress fixing.
I vote for ID, lastly because more people use it. Both from writer/designer standpoint, as well as a printing staindpoint. ID just rocks.
I posted the question on another forum at a different site and I got 14 views, 0 replies. Here, I have 51 views, 0 replies. 8O 
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