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A new update was rolled out today (2013-12-10), bumping the game up to version 1.04 and adding some new features. The changelog states:

• there is now a festive new evolving upgrade in store


• reindeers are running amok (catch them if you can)


• added a new option to warn you when you close the window, so you don't lose your un-popped wrinklers


• also added a separate option for displaying cursors


• all the Halloween features are still there (and having the Spooky cookies achievements makes the Halloween cookies drop much more often)


• oh yeah, we now have Cookie Clicker shirts, stickers and hoodies (they're really rad)

But what exactly has changed? What new upgrades and achievements are there and how do I use/unlock them?

New Cookies

If you've earned 99999999999999 cookies, it unlocks:

• 
  Gingerbread men - multiplier +25% - 9999999999999999 cookies


• 
  Gingerbread trees - multiplier +25% - 9999999999999999 cookies

Reindeer

Just as wrinklers will randomly popup, now so will Reindeer. Click on them to get:

• 1 minute of cookie production, or 25 cookies - whichever is highest. (x2 with Ho ho ho-flavored frosting)


• Random cookie unlocks:
  
  
  
  
  • 
    Christmas tree biscuits - multiplier +20% - 252525252525 cookies
  
  
  • 
    Snowflake biscuits - multiplier +20% - 252525252525 cookies
  
  
  • 
    Snowman biscuits - multiplier +20% - 252525252525 cookies
  
  
  • 
    Holly biscuits - multiplier +20% - 252525252525 cookies
  
  
  • 
    Candy cane biscuits - multiplier +20% - 252525252525 cookies
  
  
  • 
    Bell biscuits - multiplier +20% - 252525252525 cookies
  
  
  • 
    Present biscuits - multiplier +20% - 252525252525 cookies
  
  
  
  


• Achievements:
  
  
  
  
  • 
    Oh deer - pop 1 reindeer
  
  
  • 
    Sleigh of hand - pop 50 reindeer
  
  
  • 
    Reindeer sleigher - pop 200 reindeer
  
  
  • 
    Let it snow - Collect all Christmas-themed cookies above - Increases the chance of Christmas-themed cookies dropping.
  
  
  
  

"SPECIAL THINGS AND STUFF"

If you've earned 25 or more cookies, it unlocks the upgrade:

• 
  A festive hat - 25 cookies - unlocks:

A new section in the code ("SPECIAL THINGS AND STUFF") defines a Santa object that sits in the bottom left of cookie clicker is unlocked by A festive hat. You spend cookies to unlock new levels. They are as follows:

• 
  Festive test tube - You start here after purchasing A festive hat.


• 
  Festive ornament - 1 cookie


• 
  Festive wreath - 4 cookies


• 
  Festive tree - 27 cookies


• 
  Festive present - 256 cookies


• 
  Festive elf fetus - 3125 cookies


• 
  Elf toddler - 46656 cookies - unlocks the Coming to town achievement.


• 
  Elfling - 823543 cookies


• 
  Young elf - 16777216 cookies


• 
  Bulky elf - 387420489 cookies


• 
  Nick - 10000000000 cookies


• 
  Santa Claus - 285311670611 cookies


• 
  Elder Santa - 8916100448256 cookies


• 
  True Santa - 302875106592253 cookies


• 
  Final Claus - 11112006825558016 cookies - unlocks the All heil Santa achievement.

For each Santa level purchased, you will gain in random order one of the following upgrades for purchase:

• 
  Increased merriness - multiplier +15% - 2525 cookies


• 
  Improved jolliness - multiplier +15% - 2525 cookies


• 
  A lump of coal - multiplier +1% - 2525 cookies


• 
  An itchy sweater - multiplier +1% - 2525 cookies


• 
  Reindeer baking grounds - Reindeers appear twice as frequently - 2525 cookies


• 
  Weighted sleighs - Reindeers are twice as slow - 2525 cookies


• 
  Ho ho ho-flavored frosting - Reindeers give twice as much - 2525 cookies


• 
  Season savings - buildings are 1% cheaper - 2525 cookies


• 
  Toy workshop - upgrades are 5% cheaper - 2525 cookies


• 
  Naughty list - Grandmas are twice as productive. - 2525 cookies


• 
  Santa's bottomless bag - Random drops are 10% more common (special cookie unlocks from wrinklers and reindeers) - 2525 cookies


• 
  Santa's helpers - Clicking is 10% more powerful - 2525 cookies


• 
  Santa's legacy - multiplier +10% per Santa's level (1-15) - 2525 cookies


• 
  Santa's milk and cookies - Milk is 5% more powerful - 2525 cookies

For purchasing the last Santa level, you will also unlock the upgrade:

• 
  Santa's Dominion - multiplier +50%, buildings are 1% cheaper, upgrades are 2% cheaper - 2525252525252525 cookies

Cosmetic

There are a few purely visual changes that are happening:

• Snowflakes in the cookie stream


• Elf grandmas are mixed in with the Grandmas


• Wrinklers display a winter variety


• If you have 1000 or more cookies baked, the following news stories appear at the top:
  
  
  
  
  • bearded maniac spotted speeding on flying sleigh! Investigation pending.
  
  
  • Santa Claus announces new brand of breakfast treats to compete with cookie-flavored cereals! "They're ho-ho-horrible!" says Santa.
  
  
  • "You mean he just gives stuff away for free?!", concerned moms ask. "Personally, I don't trust his beard."
  
  
  • obese jolly lunatic still on the loose, warn officials. "Keep your kids safe and board up your chimneys. We mean it."
  
  
  • children shocked as they discover Santa Claus isn't just their dad in a costume after all!
    "I'm reassessing my life right now", confides Laura, aged 6.
  
  
  • mysterious festive entity with quantum powers still wrecking havoc with army of reindeers, officials say.
  
  
  • elves on strike at toy factory! "We will not be accepting reindeer chow as payment anymore. And stop calling us elves!"
  
  
  • elves protest around the nation; wee little folks in silly little outfits spread mayhem, destruction; rabid reindeers running rampant through streets.
  
  
  • scholars debate regarding the plural of reindeer(s) in the midst of elven world war.
  
  
  • elves "unrelated to gnomes despite small stature and merry disposition", find scientists.
  
  
  • elves sabotage radioactive frosting factory, turn hundreds blind in vincinity - "Who in their right mind would do such a thing?" laments outraged mayor.
  
  
  • drama unfolds at North Pole as rumors crop up around Rudolph's red nose; "I may have an addiction or two", admits reindeer.
  
  
  
  

WARNING: Spoiler-heavy answer

There are exactly 25 new upgrades, nine of which are cookies, and 6 new achievements. There are also the new reindeer and Santa game mechanics.

To start everything off, you need to purchase an upgrade called "A festive hat," which costs 25 cookies. This will unlock an icon below your cookie.

Santa mechanic

The icon reflects Santa's level and starts at "Festive test tube." It can be upgraded for 1 cookie to reach the next level. The next level will cost 4 (2²) cookies, then 27 (3³), up to its final level, which will cost 14¹⁴, a little over 11 quadrillion cookies.

Whenever you upgrade Santa's level (including the time you purchase the festive hat), you will unlock a random upgrade, which cost 2,525 cookies each:

• Increased merriness - Cookie production multiplier +15%
  


• Improved jolliness - Cookie production multiplier +15%
  


• A lump of coal - Cookie production multiplier +1%
  


• An itchy sweater - Cookie production multiplier +1%
  


• Reindeer baking grounds - Reindeer appear twice as frequently
  


• Weighted sleighs - Reindeer are twice as slow
  


• Ho ho ho-flavored frosting - Reindeer give twice as much
  


• Season savings - All buildings are 1% cheaper
  


• Toy workshop - All upgrades are 5% cheaper
  


• Naughty list - Grandmas are twice as productive


• Santa's bottomless bag - Random drops are 10% more common¹
  


• Santa's helpers - Clicking is 10% more powerful
  


• Santa's legacy - Cookie production multiplier +10% per Santa's levels²
  


• Santa's milk and cookies - Milk is 5% more powerful
  

A final upgrade costing 2,525,252,525,252,525 cookies is then unlocked once Santa reaches his final form:

• Santa's dominion - Cookie production multiplier +50%. All buildings are 1% cheaper. All upgrades are 2% cheaper.

_{¹ Christmas-themed cookie drops from reindeer
² Stacked in additive fashion, eg: +10%, +20%, etc.}

Reindeer mechanic

There are also reindeer. They work like golden cookies (and a bit like Wrinklers), in that they will appear at random intervals³, hopping across the screen. You then have to click them before they disappear. When you do that, they will give give you one minute's worth of cookie production⁴ (CPS*300) or 25 cookies, whichever is highest.

Clicking on reindeer also has a 20% chance⁵ of unlocking one of the seven Christmas-themed cookies. Each of them costs 252,525,252,525 cookies and give you a +20% cookie production multiplier. Note that similar to Halloween-themed cookies, if you already have the cookie it will not unlock a new one. This makes them harder to get the more you have.

There are also two new cookies ("Gingerbread men" and "Gingerbread trees") that automatically unlock once you've earned 99,999,999,999,999 cookies. They cost 9,999,999,999,999,999 (10 quadrillion) cookies each and give you a +25% cookie production multiplier.

_{³ Between three and six minutes; twice as frequently if you have the "Reindeer baking grounds" upgrade
⁴ Stackable with frenzies (ie: popping a reindeer during a frenzy will give you more cookies)
⁵ If you have the "Let it snow" achievement, it's a 40% chance. This means if you reset the game it will be easier to unlock them.}

New achievements

There are six new achievements. All of them are regular achievements, which means they give milk.

• Coming to town: Reach Santa's 7th form
  


• All heil Santa: Reach Santa's final form
  


• Let it snow: Unlock every Christmas-themed cookie
  


• Oh deer: Pop 1 reindeer
  


• Sleigh of hand: Pop 50 reindeer
  


• Reindeer sleigher: Pop 200 reindeer
  

• Buncha upgrades, mostly giving more CPS and altering reindeer (along with a few other things)


• New Lucky-cookie-like object, reindeer - give many bonus cookies


• A few more achievements related to "upgrading Santa" (and clicking on the reindeer; I've only unlocked "click a reindeer" and "partially" then "fully upgrade Santa")

To unlock: there'll be a 25-cookie upgrade, the christmas hat. Then, upgrade the test-tube in the bottom-left through stages of pre-elf, elf and Santa until one reaches "True Santa"; each increase in Santa-level will grant at least one upgrade for purchase.