So far, the following has been recommended:

-an index for the manual
-a tech tree foldout
-reference cards
-tech tree viewer with the help files
-no instruction manual at all, just have it on disk (definitely up for debate)
-a research goal option (similar to Civ II)
-scripting explanations/help files (similar to Fantastic Worlds)
-brief historical bit on each civ in the instruction manual

Welcome aboard! This is one of my favorite topics. I'm one of those guys who actually likes to read the manual before I play (imagine that!). Here's an important one:

An INDEX!!!

I shall simply refer you to SMAC's manual to see what confusion a missing index can cause.

Also, Travatian, I forgot to mention: You'll need to keep track of all the names of people who post ideas in your threads. That's a vital part of the Lists that will be sent to Brian. Paperwork, I know!

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CIV3 DEVELOPMENT LIST COORDINATOR

Index cards would be cool; I'm not sure how much I would use them because I haven't had any experience there. My first impression is that it would be too hard to find the specific card you're looking for in that big stack. Still, the concept is out there -- Maybe there's a way to pull it off.

One would have terrain improvement breakdown, detailing the effects of each type of improvement on each type of land, as well as time frame; the back side could show combat modifiers, the various chasis, weapons and armor upgrades and unit special abilities.
The second card could list the various SE choices, since from reading some of the other posts, a lot of people want more options when it comes to this, so this card could show the combinations; on the back it could have the factions listed with a very brief bio on them (agression level, starting techs, goals, etc)

And a third which both sides would simply list all of the techs alphabetically, and the affects each one gives, similar to what pops up when you learn the tech (new city improvements, units, wonders, etc).

As far as the index for the manual, at this point I'd say there is no debate.

The II manual was all techie, and boring. How to move a unit. How to change the production. However, the original manual was actually fun to read. It had little historical bits, which is a real necessity for a historical game. It gave context, and a sense of atmosphere to the game, more so than was present in the sequel.

What is everyones feeling as far as the learning scenarios in SMAC, the Explore, Build, Conquer ones. Also, the walkthru's of the various screens (city screen, design workshop screen, etc).

Should these be included in CIV III?

Any changes? More info, less info?

Is this something everyone thinks should be included in a seperate manual? Wait until a CivIII expansion?

Note: If the game comes with HTML help, I'm going to return it.

Use a voice like Churchil for the units.
Use a voice like Einstein for the discoveries.
...

Use a personage for the tutorial that speaks. This is more funny then a text.

I would like to see the manual contain a little about where one might find interesting things about civilization history. Maybe a page in the back that says:

If you like this game, you might be interested in these books about history:

I realize that may be a somewhat... thick manual but I think that when the player is in front of the game she/he should devote the whole of his/hers attention playing not trying to find out what the manual didn't include. (for example what does the republic do in terms of economy and so on).
And having a complete manual of CIV to read at your leasure is a really a welcomed luxury

Also there has to be clarity and easy of use in the manual. Sections and subsections for everything much be clearly categorized. CIV 2 manual is really mediocre. A nice example would be the Alpha Centauri manual.

That is my humble opinion