As far as I know there are 343 Common/Skill Books in Skyrim (there are absolutely more, these are just the ones I know of).
Not even counting the Journals and Miscellaneous logs which I know of (50).
And counting the Spell Tomes
I know of (89, and yes, I personally would love to have a collection of those too), there is an approximate total of 482 books in the whole game (surely more).
I have the house in Markarth which has 3 bookshelves with 3 shelves each, each one of those bookshelves can house a total of 54 books, so in total the house can have 162 books in display, this is the house with the most space for books (not counting the fact that you can save books in chests but thats not the point here).
So, in the end you are going to need some House mods when the creation kit comes out.
I just hope you got the PC version, because when the kit comes out I will look forward to a "library in your house" mod.
P.S.
I have the complete list of books I have knowledge of, if you want it feel free to send me an email (I put it as my website in my profile).
gaming.stackexchange.com/users/15304/Mars
Windhelm House has in fact 12 shelves, each capable of holding 11 books.
There are four bookshelves (with 2 shelves each) and one taller bookshelve (with 4 shelves) with the total of 12 shelves, the house can hold 132 books.
I just bought that house in order to get the Windhelm Home Decorating Guide book.
Edit:
Alright, I own 4 houses in Skyrim, so here im listing the houses and its book space numbers (Only Interactive bookshelves).
Whiterun - Breezehome: 47 Books Riften - Honeyside: 72 Books Windhelm - Hjerim: 132 Books Markarth - Vlindrel Hall: 162 Books Solitude - Proudspire Manor: 132 Books Thats it.
Detailed Info:
Whiterun's Breezehome: Livingroom - 1 Bookshelf with 2 shelves (18+18), Alchemy Lab - 1 Bookshelf with 2 shelves (11+11).
Riften's Honeyside: Bedroom - 1 Bookshelf with 2 shelves (18+18), Basement - 1 Bookshelf with 2 shelves (18+18).
Windhelm's Hjerim:
By the stairs - 1 Bookshelf with 2 shelves (11+11), Secret Room - 1 Bookshelf with 2 shelves (11+11), Kitchen - 1 Bookshelf with 2 shelves (11+11),
Armory - 1 Bookshelf with 2 shelves (11+11), Bedroom - 1 Bookshelf with 4 shelves (11+11+11+11).
Markarth's Vlindrel Hall:
In front of Alchemy Lab - 3 Bookshelves with 3 shelves each (18+18+18 + 18+18+18 + 18+18+18).
Solitude's Proudspire Manor: I havent bought the house yet, but I will when I have the money, in the meantime according to Ricky, the house has 6 bookshelves with 2 shelves each.
11
X 6
X 2 = 132.
gaming.stackexchange.com/users/15304/Mars
Installation of the Hearthfire DLC means that Vlindrel hall is no longer the optimum house for your master book hoarder.
The ideal construction options for building a house to maximise the storage of books:
Small House / Porch: 0 Books Main Hall : 1 ×
Large Bookcase (54 books) =
54 books East Wing - Library : 4 × Small Bookcase (22 books each) = 88 books 5 × Medium Bookcase (44 books each) =
220 books West Wing - Any Option : 0 Books North Wing - Any Option : 0 Books
This means that a single Heathfire homestead can accommodate 362 books on shelves - more than double the capacity of the houses in the base game.
Unfortunately, this means that using the numbers in Mars' answer
this huge capacity still isn't enough to collect every book in the game.
gaming.stackexchange.com/users/16659/Rory
I haven't seen the house in Windhelm due to a bug keeping me from buying it, but I know the house in Markarth (8000g) has 3 bookshelves with 3 shelves each, capable of holding 18 books per shelf.
It seems to be the one with the most bookshelves.
But, I can't remember how many were in the house in Solitude...
gaming.stackexchange.com/users/14775/Niro
Windhelm has the most bookcases with 12.
Although you either have to be on the stormcloak side and have gotten to the Fort Neugrad mission or have defeated the stormcloaks on the imperial side in order to buy it. http://www.uesp.net/wiki/Skyrim:Houses
gaming.stackexchange.com/users/15685/JIW
I'm an avid book collector, and I was wondering what house has the most bookshelves in Skyrim. I currently only own the Whiterun house, which has 2 bookshelves of 2 shelves each.  Is there a house I could buy that has more bookshelves?  Edit  Since not all bookshelves hold the same number of books, I'm looking for the house that has the most spaces on bookshelves for books, not necessarily the most bookshelves
What house has the most bookshelves?
gaming.stackexchange.com
<the-elder-scrolls-5-skyrim>
gaming.stackexchange.com/questions/37520
gaming.stackexchange.com/users/8462/Rachel
The house in Markarth can have 162 books, a Heathfire homestead can hold 362 books and Windheim has the most bookshelves with 12. The community offers detailed descriptions regarding the houses and the storage capabilities, when it comes to books. The biggest one seems to be tied with DLC content.
Players listing the houses with the most book storage capacity.