For one thing, "two thousand" is shorter to say than "twenty hundred".
600: six hundred 601: six oh one (shorter than six hundred one) 1899: eighteen ninety-nine (shorter than one thousand eight hundred ninety-nine) 1900: nineteen hundred (shorter than one thousand nine hundred) 1901:
nineteen oh one (shorter than nineteen hundred one, shorter than one thousand nine hundred one) 1999: nineteen ninety nine (shorter than one thousand nine hundred ninety-nine) 2000: two thousand (or 2 "K"?)
(shorter than twenty hundred) 2009:
two thousand nine (shorter than twenty hundred nine) 2010: twenty ten (shorter than two thousand ten)
Basically when the number has three zeros it is shorter to say "thousand" than "hundred".
Once there are fewer than three zeros it is shorter to say "Y thousand X" for Y00X and "Y hundred X" for YYXX.
This usage isn't limited to years either.
Any numbers in the same range will have the same kinds of contractions.
There is a Simpsons episode where this is played for laughs, when they need eighty-five-hundred dollars to fix their roof, and they only have $500, and Homer whines that they still need eighty-hundred.
english.stackexchange.com/users/380/Mr. Shiny and New 安宇
There are no rules, only loose conventions, formed for brevity, convenience and ease of mental parsing.
The convention has been modified for the years 2000-2009 (two thousand and nine), just as it has for 1000-1009, probably for the reason Nav mentions - it just parses nicely that way to an English speaker.
You can expect every year from 2010 (twenty-ten) onwards to soon revert to the conventional form in common parlance, which has the advantage of being shorter and distinguishes centuries from one another very clearly.
Worth noting is the fact that the years 1-999 are usually suffixed with "AD" to make it clear that we are talking about a year rather than an arbitrary figure.
Post-1000 years do not require this verbal signposting as the use of this unusual convention makes it clear that these are years.
english.stackexchange.com/users/1542/PyroTyger
In England we say "two-thousand-and-one" not "two-thousand-one" etc.
Most people say twenty-eleven, twenty-twelve, but I'd say there was a 50/50 split between 'two-thousand-and-ten' and 'twenty-ten'.
english.stackexchange.com/users/8867/Stephen Phillips
The logic apparently lies in grouping the digits in a way that's easy to visualize (mentally) and/or pronounce.
Since there are always two zeroes in nineteen hundred, saying 'hundred' makes sense.
2000 has three zeroes, which is visually easier to recognize and split as two and 'thousand'.
Reg has given an example.
There don't seem to be any other logical reasons for this trend.
english.stackexchange.com/users/2294/Nav
I think the main reason is a rhythm of pronunciation.
That's why we use "two thousand ..." instead of "twenty ...".
Also I have heard a two songs with "two thousand twelve".
So the change will occur in 2013.
english.stackexchange.com/users/2312/vortexwolf
We pronounce 1923 as nineteen twenty-three; but 1900 as nineteen hundred. Why isn't year 2000 pronounced as twenty hundred instead of two thousand?  What are the rules for pronunciation of years in English? Does it change according to the first two digits of year? Could you give examples for special cases, if any?
What are the rules for pronunciation of years in English?
english.stackexchange.com
<pronunciation><dates>
english.stackexchange.com/questions/5442
english.stackexchange.com/users/127/Mehper C. Palavuzlar
It appears that there are no fixed rules for how to pronounce years, although there are patterns which are generally justified based on what is easier for people to visualise or pronounce. For example, when a year has three zeros, it is shorter to say "X thousand". Similarly, when a year has two zeros at the end, it is easier to say "X hundred". It is shorter to say "two thousand" than "twenty hundred". If the number has 3 zeros is it shorter to say "thousand" than "hundred". The usage isn't limited to years.There are no rules, only loose conventions for ease of parsing. In England a different form "two-thousand-and-one" is used. It is just the grouping of the digits that makes it easier to memorise.
It appears that there are no fixed rules for how to pronounce years, although there are patterns which are generally justified based on what is easier for people to visualise or pronounce. For example, when a year has three zeros, it is shorter to say "X thousand". Similarly, when a year has two zeros at the end, it is easier to say "X hundred". Basically when the number has three zeros it is shorter to say "thousand" than "hundred". There are no rules, only loose conventions, formed for brevity, convenience and ease of mental parsing. The logic apparently lies in grouping the digits in a way that's easy to visualize (mentally) and/or pronounce with a rhythm.. 
The convention has been modified for the years 2000-2009 (two thousand and nine), as it just sounds better that way to an English speaker. When the number has three zeros it is shorter to say "thousand" than "hundred" and once there are fewer than three zeros it is shorter to say "Y thousand X" for Y00X and "Y hundred X" for YYXX. This is largely due to rhythms of speech. It appears that there are no fixed rules for how to pronounce years, although there are patterns which are generally justified based on what is easier for people to visualise or say out loud. For example, when a year has three zeros, it is easier to say "X thousand". Similarly, when a year has two zeros at the end, it is easier to say "X hundred".
It is shorter to say "two thousand" than "twenty hundred". If the number has 3 zeros is it shorter to say "thousand" than "hundred". The usage isn't limited to years. There are no rules, only loose conventions for ease of parsing.  In England a different form "two-thousand-and-one" is used.
Basically when the number has three zeros it is shorter to say "thousand" than "hundred". There are no rules, only loose conventions, formed for brevity, convenience and ease of mental parsing.   The logic apparently lies in grouping the digits in a way that's easy to visualize (mentally) and/or pronounce with a rhythm..
The justification for pronouncing years in one way or another is generally related to what is easier say and visualise. There do not appear to be any fixed rules for this. When a number has three zeros, it is easier to say "X thousand" and when there are two zeros it is easier to say "X hundred".