If it can be counted as an instruction manual, the biggest ones I've owned were the strategy guides that came with the Starcraft Battle Chest. Granted, over half of the manual for both games consisted of a guide for each and every mission (though I still can't beat the fucking Norad II mission...), but there is still a hefty bit of informational text on the units, general strategies, etc. In total, it's 212 pages of reading for both games, in two softcover books.
If those don't count, then the manual for Roller Coaster Tycoon 3 was insanely long. The manual itself is about 100 pages, with no guides or anything, just stuff about how to play the freaking game. Come to think of it, though, that game deserved it, I never played it to its full potential: It's a huge game, with a lot you can do.