Plural of flagship; the main ships in a fleet that carry the commanding officer, or more generally, the most important or prominent things in a group.
From 'flag' (Scandinavian origin) plus 'ship' (from Old English 'scip'). A flagship is literally the ship that flies the admiral's flag, and the term has been extended metaphorically to mean 'the most important one.'
The metaphorical use of 'flagship' is brilliant—we now talk about 'flagship products,' 'flagship stores,' and 'flagship universities,' all using the naval concept of the chief vessel to mean 'the most important or representative example'!
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