It would really depend on the context. If I'm talking about something that happened in a certain year or if I'm refer to the state of the world in a certain year, I would use "in."
"In the year 2000, George Bush was elected President."
"In the year 2000, 5% of the U.S. population was unemployed." (statistic invented)
"In the year 2000, I was still in high school."
I would use "for" if referring to something that lasted the entire year.
"For the year 2000, I made a New Year's resolution to lose weight."
"For the year 2000, McDonald's gave out free French fries every Friday."
There are also many other situations that these phrases could apply! Wait for other people to post most examples and contexts.