We're shortly going on our first fly drive in Greece (Peloponnese), after loads of packages to various bits of Greece. We're flying to Athens and then spending 3 nights in Nafplion, 3 in Monemvassia, 3 in Paralio Astros and the last night near the airport. The first 2 lots of accommodation were booked using
http://www.yourgreece.gr who have some lovely and unusual places throughout Greece that might be worth checking out.
There are some lovely and unspoiled places in the Peloponnese - I agree with the previous posters about the Mani and Gialova but also quite fancy staying at Koroni or Methoni, in addition to the ones I've booked this time. You could also look at the Pelion, another beautiful area, or try Tapestry holidays who specialise in "uncommercial" areas.