We will be taking the ferry to Santorini, but flying with Aegean after that. We generally take only our carry-on backpacks and another small one. No problem on overseas flights, but weight limits on Aegean (and I know other European airlines). Will the planes be too small for the backpacks to go into overheads (soft-side, no wheels). I'm still hesitant to check them. Will Aegean actually weight them??
For economy class, you can check in bags weighing up to 20 Kilos (about 44 pounds). You're allowed to carry one item with you on the plane weighing not more than 8 Kilos (18 pounds). Check their website.
http://en.aegeanair.com/travel-information/baggage/epitrepomena-oria-aposkeuonheiraposkeuon/
I would not be concerned about checking a bag. Keep in mind you are flying point to point, so very little chance of losing a bag. Most of the airports are also small, getting your bags is easy.