That makes me sad... I got my BG in a 4 in 1 boxset which had no manual! Argh!

My favourite is the Arcanum manual.
I think its close to 200 A4 Pages long and is presented in a bit of an olden style newspaper format. Even the writing style is in character. The Glossary was invaluable for information on the races and world history.
I say 200 A4 pages because I've only had the privilege of it in PDF form in a small box re-release and had to print it all out to get the best of it.
I never really liked the copy protection schemes manuals descended into (like that #@!$ing code wheel on Rocketeer. I recall rather vividly the Sam n' Max dress ups images too so I guess they're memorable if not fondly remembered.

I'm quite satisfied with PDF manuals; while they aren't something to carry around (not without a portable PDF reader, anyway), they give an extra incentive for playing the game (I remember always finding myself playing some Icewind Dale after reading about the various weapons, armor and neat D&D Spells in it one by one, escpecially if I would have had to do something else ;-)).
However, I find today's few-pages, tell-nothing manuals lacking; particularly for games that just CRY OUT for a manual (*cough-Anno1404-cough*).

Indiana Jones and the Last Crusade - the graphic adventure version - had an awesome manual, presented as Henry Jones' holy grail journal, full of handly written notes and drawings, giving depth to the game and a better connection with the movie.
Flashback had also a good manual, giving a lot of details and life to the futuristic universe of the game.
Cruise for a Corpse manual was litterally the inspector's notebook, with paper cuts concerning the other passengers of the cruise, and also a beautiful map of the boat.
I really loved manuals back then, it was a great way to give more depth to universes presented in the games at that time.
And I'm not even talking about manuals that were actually required to play the game correctly. No, I'm not talking about copy protection, but many games had no tutorial levels or even a clear picture showing the controls.
Take the original X-Wing for example: if you don't have manual or just the reference card to learn all the keys, even the first missions can be a nightmare.

My favorite manuals include the spiral-bound books for Aces of the Pacific, Aces Over Europe, and Secret Weapons of the Luftwaffe, all providing great history lessons about the campaigns, aircraft and fighter tactics of WWII. The hard-core craziest manual in my collection is the glossy, three-ring binder for Falcon 4.0 -- 26 chapters plus appendices! More Microprose manuals on my shelf are the books for Silent Service II (US Navy submarine offensive that strangled imperial Japan), Across the Rhine (tanks in Europe) and European Air War. All these manuals are timeless, which is why I'll never part with them.

Yeh, man, things like cloth maps really added something to a game. It's all part of the art, the presentation, and made some games very special in that way.
It's the difference between a frozen dinner and a fine restaurant.

Starsiege.
2 Huge books.
One giant manual with all the information you'll ever need to play the game, including the specs of every herc and weapon, and one book with backstory and illustrations.
Even had definitions of computer terminology in the glossary.
EG: Tcp/Ip, dial-up, graphics cards, sound cards, bit depth, directx, etc.
Also, myth2, descent2, force commander, dark forces2.

As I said on another topic, I love reading manuals. They're the perfect thing for toilet reading.
Some good manuals (as I remember):
Homeworld (Such a cool and detailed backstory on there)
Civilization IV (A great way to learn about the game for civ newbies)
NeverWinter Nights
Sacrifice
Diablo II
Dungeon Keeper 2

Atlus is one company keeping this stuff alive, and they smell their manuals too:
http://www.youtube.com/watch?v=Rhlr1tAqljk
:D

hmm, think about that: mostly when a game gets released they try to sell you a "strategy guide" along with it. which is mostly ridiculously overprized, costing almost as much as a pc game. Imo this is where all the cool manuals and hintbooks went. into another money-making franchise alongside the "normal" game releases, all encouraged by the publishers.
old classic manuals were: Baldurs Gate2, Railroad Tycoon, Civilization, Starcraft (!), Street Fighter on the C4 had a 200page manual, Sim City 2000, Fallout 2 (spiral notebook), monkey island 2 (with voodo mixing wheel), .....
nowadays you get an installation instruction with advertisments for the strategy guide

I'm starting to notice a disturbing trend... *shudders*

I am quite a fond of the old 'Lords of Magic: Special Edition' box, so nice, so large - So much back story and character.

I was a big fan of the Baldur's Gate II manual -- always good for a toilet read

A tear comes to my eye when I think about how much I miss those thick manuals. Two come to mind right away. M1A1 Tank Platoon. So much info, and you had chapters on Russian military doctrine, training, etc. Start the game wondering why your guys got blown up, but after reading the manual and playing more, you'd be echelon lefting and righting, using hull down, etc. Man.
The other is Civilization. Here was a case where the game was so ungodly good, it fed into the manual, and the manual fed back into the game, in a vicious circle of awesomeness. Read the manual, want to play the game. Finish a game, want to read the manual.