Perishable commodities are those that cannot be stored indefinitely. While in space (but not while landed), these commodities will slowly degrade one unit at a time until they are all gone. Items listed as "Highly perishable" will do the same thing, only faster. Try to carry these on short routes so you don't lose too many.
All commodities have a "health bar" at the bottom. In perishable and highly perishable commodities, this bar slowly decreases over time. If it reaches zero, one unit if the commodity decays to nothing and the bar resets itself. Given the flat rate of decay, it is recommended that perishable commodites be shipped in large quantities, so that the loss makes up a small percentage of your total haul.
The health bar works independently for each perishable commodity. Half-decayed units of a commodity sell for full price. Commodities spoil even outside your ship; in other words, if you're mining the stuff, tractor all loot immediately. Trying to cheat by only collecting your loot when you're ready to leave will actually backfire on you.