Parikia -- The port town has three basic hotel zones: agora (the market area), harbor, and beach; alas, all can be very noisy. Here are some suggestions for potentially quiet places to stay. In addition to the places listed here, the Pandrossos (tel. 22840/22-903; www.pandrossoshotel.gr), on a hill overlooking Parikia and the harbor, has a pool and a quiet location. The hotel is within walking distance of town, but on hot days -- with apologies to Al Gore -- I'd rather drive up the hill; doubles from 130€ ($169).
Naoussa -- You might consider the coyly named Heaven Naoussa, (tel. 22840/51-549; www.heaven-naoussa.com) with 4 doubles, 5 suites, and 2 maisonettes (with pool); doubles from 110€ ($143); suites from 150€ ($195); maisonettes 1,600€ ($2,080) per week. The architecture is, appropriately, Cycladic, the decor is eclectic and stylishly casual, restaurants and the harbor are steps away. If you're unable to find a room, try Nissiotissa Tours (tel. 22840/51-480), just off the east (left) side of the main square.
Lefkes -- The Lefkes Village Hotel is quite special, but if it is full when you visit, or if you want to spend less, the 14-unit Pantheon (tel. 22840/41-646) is perfectly decent and a lot cheaper; doubles from 60€ ($78).