Personally I love a nice game manual. I love being able to open the game for the first time, take the manual and gently flick through the pages the side of the manual, allowing the smell to escape and elate my nose 
Come to think of it.. I am actually dissapointed when a 5 pager is slapped into the front cover, or even NONE AT ALL!!
The Game manual should form part of the game. First and foremost this to me means adding a lot of lore to the game, which will allow the player to be immersed into the game so much more! This lore can include the prelude, descriptions of main characters / races, and even more info on important NPC's, gods, locations etc.
Also, it should contain some Basic information on the workings of the game. An "overview" of how to play - so to say.
This does not include advances strategies and map layouts etc - those can be covered by the overpriced "Strat-Guides" you mentioned (which, I must admit, can be very helpful for hard-core players of any particular game).
Finally, it should give the player good / extensive information on unit's / items / buildings.
I always believed any game should have essence, and a well designed manual add's so much more to the feel of the game itself.
Take 'Galactic Civilizations II' manual for instance.
- (Avg)
Very basic lore to give you somewhat of an idea of the story and races.
This is acceptable since ingame has far more intel on the different races.
I would generally expect at least 1 page to have the prelude of the game storyline, and 1/2 a A5 page dedicated to the lore of each race / hero / important NPC etc.
- (Good)
Extensive overview of the game mechanics, screen functionalities/interface etc.
This is a must for any game genre
(-) Some items could rather have been included under the tutorials section of the game itself or as a PDF
This would have left a lot of space open for items lefts out (see below). These sections include items
such as: Creating a game / ship / race.
- (Terrible)
There are no manufacturable weapons listed!! And where is the tech trees! This is sacraledge!
I would have expected at least 1 dedicated to each of the tech channels.
Also, an icon, description, any pre-requisites of any item which will have been made available by the specific tech-channel should have followed this. This would have allowed me (as a newbie) to overview what the game offered, and which tech tree would best suite my needs, and plan future deep-tech routes.
So in review, I believe a manual should have the following:
- Great look and feel - utilise some of the in-game interface (text boxes, caption fonts etc)
- Add a good amount of lore to have the player connect to the game characters / races / etc.
- Give a great overview of the interface and basic gameplay mechanics
- Show techs, weapons, buildings, etc. wich will be offered by the standard game, with descriptions/costs/etc.
- Standard additional info such as : Warnings, SysReqs, Contacts and Credits
Oh, and I also believe that there should most definately BE a manual, hard-copy and electronic (PDF).
Strategy guides are still viable, but I believe them to be just that... strategy guides.
A game manual should give enough information to the newbie player to have a firm knowledge of how to use the game and what to expect from it (tech trees etc). Strategy guides are meant for the hardcore players to analyse statistics, determine "best" ways, have walkthroughs etc etc.
As for the in-game method, Any "process tutorials" should be included in game (or PDF). No need to laden the manual on such processes if you can just have it shown to you directly in game.
I don't believe gamers should be 'Guided'. Thats the fun in the Game, to figure it out. You simply need to know where to start 
In short - more essence, less hand-holding.
Njoy!