The difference between whiskey and whisky is simple but important: whisky usually denotes Scotch whisky and Scotch-inspired liquors, and whiskey denotes the Irish and American liquors.
The word itself (both spellings) is of Celtic origin, and modern whisky/whiskey distillation practices originated in Ireland and Scotland. Using whiskey to refer to Scotch whisky can get you in trouble in Scotland.
Examples
In November, China ruled that any product labelled as “Scotch whisky” in China must be made in Scotland. [Financial Times]
There’s no better place to learn about and enjoy whiskeys, and to meet the whiskey makers themselves. [Nashville Scene]
Chivas, the luxury brand of blended Scotch, recently conducted a survey soliciting consumer views on whisky age. [The Globe and Mail]
For starters, he quoted federal regulations (Title 27, section 5.22) about what constitutes bourbon whiskey, rye whiskey, malt whiskey, wheat whiskey, and malted rye whiskey. [Seattle Weekly]