Writing this has been on my agenda for a few days, but after arriving home in Paris, then seeing my room mate off to Berlin, I have had a rather unproductive batch of activity, colored by a mild cold (which seems to have been Greece's parting gift).  At any rate, here come some tidbits about the trip, bullet-style.

• Since Greece is primarily a series of islands, it can be hard to feel like you've had a truly representative or comprehensive tour of the country if you don't have two weeks to explore and island hop.  Five days was barely enough time for Athens and Santorini.  We could have easily stayed on the island for a week or more.
• Everything the travel books say about unreliable transportation in Greece is true.  Always have a back-up plan.  When we arrived at the Athens airport, the metro was out, so we had to take a 45-minute bus to a metro stop closer to the city.  That said, even when transportation was out, it was easy to find information and alternatives.
• The metro is easy to use.  It's easy to navigate; there are only a couple of lines, and just a few major stations where you can transfer.  At each stop the doors automatically open and the name of the stop is said over the speaker system.  Buying tickets is easy, too, at automated kiosks.

• Ferries are notorious for not keeping to their schedules.  We purchased tickets in advance (by about two to three weeks) using greeka.com.  Though the ferry didn't seem full when we were on it, we had trouble on the site choosing the ticket options we wanted (i.e. economy vs. business, etc.), so despite the risk, I do recommend booking early, especially if you're interested in the high speed or if you're traveling during high season.  By the time we were in Greece and ready to hop on the ferry, they had changed the ferry number, so we had to get our seats reassigned after boarding.  Also, if you're not a Greek student, you apparently don't qualify for the student discount, as we had to pay the difference once we got on board (though on the trip coming back, no one even asked to see our student IDs, so perhaps it's worth risking).  Our last full day in Santorini, our hostel owner told us that the high speed ferry hadn't arrived that day, and that it may not come the next day (when we were supposed to return to Athens).  Fortunately when we went to the ticket office the next morning to confirm its arrival, our ferry was in fact scheduled to come to the island, though again the ferry number had changed and so had our seats.  Had the ferry not come we most likely would have missed our last day (when we had planned to see everything in Athens), and possibly our flight (which required us to leave for the airport around 3AM that night).  So, as all the guide books advise, it's best to have more than one day on the tail end of your trip in case you have any boat problems.

• We chose the high speed ferry because it was significantly cheaper than a plane, still affordable, and not as long a ride as the regular ferry.  The high speeds supposedly take five hours to get to Santorini, one of the farthest islands from the mainland, though each way it took 6+ hours (about 7.5 on the way back to Athens).  If the regular ferries are as likely to take more time than noted, I'd be wary of the 12+ hour trips to the farthest islands.
• Riding on the ferries is quite comfortable, seat-wise, though there's not much of a barrier between smoking and non-smoking areas.  The fact that they even distinguish them is a step forward for Greece (all restaurants are smoking and there are no sections, smoking's allowed in the airport, etc.).  Smoking wasn't quite as omnipresent as it was in Eastern Europe -- like in Bosnia -- but it's more prevalent in Greece than in other EU countries like France, where they've banned smoking indoors.  None of us had any trouble with sea sickness on the high speed, and I'm notorious for my sensitive stomach.
• There's a snack bar on the ferry that sells chips and not-French-fresh baked goods, but if you plan to eat a meal while you're on board, you might want to consider bringing it yourself.  There aren't many options on board (mostly airport-like sandwiches).

• Greek food is ridiculously delicious.  Don't miss the yogurt and honey.  The yogurt has a texture almost like sour cream, and the honey is somehow more honeyful.  We didn't eat a single meal while we were there that was (a) expensive (especially by Parisian standards), and (b) anything but overwhelmingly delicious.  I recommend chicken with yogurt and honey sauce (really, anything that comes with yogurt and honey is win), tzatziki, oven-roasted feta with honey and sesame (again, anything with honey = something you want to eat), pastichio, any lamb dish, etc.  I didn't find any Greek donuts while I was there, which is either due to the difficulty in making them (having a donut frier), or perhaps because they are an American-Greek tradition?  Anyway, if you've ever eaten Greek food in Birmingham, Alabama, you can rest assured that you're getting pretty authentic stuff.  Except for maybe the yogurt.  It seems one can never have yogurt quite so delicious, thick, and creamy, as when one is traveling in Greece.

• There are many places to stay on Santorini.  If you're the kind of person who has an income and isn't a student scrambling for the cheapest options, I recommend staying in Oia, which was by far the most beautiful place we saw on the island.  I didn't bother to look, but I'm sure there are a number of ritzy and small hotels, spas, etc. as it is a major honeymoon destination.  There's a hostel in Oia that's 17€ per person per night, but we opted for a hostel on Perissa Beach called Stelio's Place, which I highly recommend.  It was only 8.50€ per person per night, and the rooms and service were as good as any hotel I've ever stayed in.  Perissa Beach is a little out of the way and much more secluded, but it has a great small community feel.  The hostel was literally meters from the black sand beach, and there are a number of affordable restaurants within walking distance.  The bus stop for the area is just outside the hostel, and it was easy to catch a bus to some of the larger cities and communities on the island.  I highly recommend Stelio's Place if you can put up with the other guests, who are mostly college co-eds and can be a little drunk and noisy if they're traveling in groups.  We only had trouble with noise one night, but fortunately they went out drinking around midnight and we didn't hear them after.  I suspect that during the high season there's more of this type of thing, but perhaps a good pair of earplugs is all you need.  The hostel staff is prefectly friendly and respectful, and they will pick you up and drive you back to the port for your ferry, free of charge.  During the low season (September-April), Perissa Beach is pretty quiet and secluded.

• Buses on Santorini all run to Fira, the capital of the island.  To get from any smaller city or community to any other part of the island, you must catch a bus to Fira, then transfer.  All bus tickets are purchased on the bus, and range from 1€ to ~3€ (each way).  Fira might be a good place to stay simply because you're near the main bus terminal of the island, and since it's a larger area there are more restaurants, places to stay, etc.
• While it's good to plan more than one day in Athens for the reasons I listed above, you can see most of what is there in one day, easy.  We happened to be there on the weekend of Greek Easter (a different date than Easter elsewhere), so all the monuments and museums closed at 3PM on Saturday.  Still, when we set out around 9AM we managed to see most everything, monument-wise.  Everything's pretty easily accessible by metro.  However, we didn't see any museums in Athens since the monuments were higher on our list, but had they held regular hours I think a day and a half tops would suffice.  Athens has a touristy flea market and restaurant area, and some more authentic pockets of local life, but as a city we didn't find it too exciting to walk around (as I would, say, Paris, Venice, Prague, etc.).
• Our first night in Athens we stayed at AthenStyle hostel, which was affordable and extremely nice.  Very clean, great common areas, incredible location (less than a five minute walk to the main part of town full of restaurants, shopping, etc.), easily accessible by metro, friendly staff.  It was a bit more expensive than other options but totally worth it.  Their private rooms include a kitchenette.  We didn't see it, but the guy at the desk told us they were about to complete their rooftop cafe and bar, which would have a great view of the Acropolis.
• The hostel we stayed in on our return, Hostel Aphrodite, was much less hotel-like, and much more like your average hostel/camping facility.  They had great breakfasts (not included in the room price), but the bathrooms, while clean, were a little strange, lacked hooks or shelves in the showers, etc.  The room had a sink and two bunk beds with pretty tight quarters.  It would be a good budget option if it weren't such a long walk from any metro, and in a part of town where there's nothing to see, and where, as females, we felt pretty unsafe at night (we hardly saw ANY women in the area who weren't tourists, and the men were often in big groups, though none approached us).  This was all despite good reviews of the area and the hostel.  If you're traveling with males and you don't mind a walk and a twenty-minute metro ride each way, it's a cheap place and it's not all bad.  We concluded that one reason they probably have good reviews is that you get a free shot at the bar your first night.
• As the clock moves toward midnight the night before Greek Easter, churches across the city shoot off fireworks.  This is something we discovered while trying desparately to sleep before heading to the airport around 3AM.
• I've read lots of warnings about taxis in Athens -- that the drivers are notorious for rip-offs, etc.  We managed not to use any except to get to the airport.  I think if you call to reserve a car there's no real trouble; it's primarily in tourist spots (like at the port or the airport) where the drivers will try to get you into a car so they can overcharge you.

• The metro in Athens closes on weekdays at midnight.  Our ferry was late arriving, so around 11:30 we booked it to the metro stop (a short walk from the port) and managed to make the last train.  Keep that in mind when you're booking ferry tickets -- that your ferry may be anywhere from 2-3 hours late arriving, and that after 11:30 or so, your only transportation options are night buses and taxis.
• The light in Greece is different than anywhere else I've been.  In addition to being very beautiful, the sunlight is extremely harsh.  While it seems that everyone needs reminding that without sunscreen, you will get sunburned if you lay out on a beach, my fellow travelers insisted that they tanned well and would have no trouble.  While I was religiously slathering myself with sunscreen (even if we were just sitting in direct sunlight while eating lunch), my friends were cultivating pretty wicked burns, which can be acquired in just an hour.  It's best to avoid direct sun between 12PM and 3PM especially.  With a generous application of 30SPF, though, you'll probably be fine.  It's also worth noting that sun stroke can be common, so drinking a lot of water (especially while on the islands) is advisable.  Check to see if the places you're traveling have potable water, though.  Athens certainly does, but most places on Santorini don't, since they don't have the proper desalination plants.