Start with the airport, not the map
Before you fix an island order, check which of the three has the best direct connections from where you're flying. That island should usually be first — or last.
Same islands, different order
Swapping the order you visit Paros and Santorini doesn't change the trip itself — same nights, same hotels, same ferries — only which one you fly into.
Two home airports can beat one
If you live within reach of more than one airport, flying out of one and back into another (an "open-jaw" ticket) is worth pricing separately from a simple round trip.
Compare the whole trip, not one flight
The entry airport, the island order and the return airport are three separate decisions. Check all three before booking any one of them.