Island Hopping from Athens Greece to Turkey

There are several ways that you can Island hop from Greece to Turkey. We started our journey from the port of Piraeus in Athens. This seems to be the more popular port and there is a Metro(Subway) that you can catch that drops you off right at the port which makes it fairly convinient.
The 4 main crossing points are:

1. Chios -> Çesme
   - This is the easiest route to get to Izmir, if you are trying to make your way up to Istanbul and is the closest to Istanbul.
2. Samos -> Kusadasi
   - If you are planning a trip to the popular Ephesus ruins then this is a great option. Kusadasi is a short distance(~20min) from Selculk, where the ruins of Ephesus are located.
3. Kos -> Bodrum
   - This is further south and if you are coming from some of the southern islands of Greece or are going to some of the southern towns then it may make sense.
4. Rhodes -> Bodrum, Fethiye, or Marmaris
   - If you are making your way to Fethiye then this might be a good option.

I found that in my searches for ferries there were plenty scheduled in the High Season, which is from June to September. When you get into the Low Season then is becomes a little more challenging with ferries only running on certain days, so if you have a time sensitive schedule during the off season then make sure that you plan ahead for the ferry times.
Also, I would recommend that if you are traveling during the high season that you book your ferry tickets ahead of time to make sure that you get a ticket. I traveled during the off season and it didn't seem to be a problem booking a seat at the time of departure at the ticket offices at the ports. The only onle that I did book online was an overnight ferry that I wanted to make sure that we caught and even so, when we arrived there seemed to be quite a few vacant seats and we probably could have bought our tickets the day of.
I found that the best way to plan my Island Hopping and find the schedules for the different options was to use the Fantastic Greece website & they have a link to ferries where you can put in you destinations and it will give you different options. Fantastic Greece. You can also book at http://www.ferriesingreece.com/ but, I find the Fantastic Greece site to have a better user interface.
Here is a list of the main Ferry Lines:

1. BLUE STAR FERRIES (Attica Group)
2. HELLENIC SEAWAYS
3. MINOAN LINES
4. AEGEAN SPEED LINES
5. KALLISTI FERRIES
6. DODEKANISOS SEAWAYS
7. SEA JET FERRIES
8. NEL LINES
9. GA FERRIES
10. ALPHA FERRIES

If you are interested in more information about the different ferry lines you can visit: Ferry Line Details.

One other note is that if you are looking to get from Izmir to Istanbul I found that there is a local airline that can offer some pretty cheap rates.  It is called IzAir.  It would have taken me 8-10hrs by train or bus to get from Izmir to Istanbul and cost $35(US) by train or bus but, instead I got a one way ticket from IzAir for $27(US) and I was there in an hour and a half.  Pretty sweet deal!

There are some great books on the Greek Islands and as usual, I am a huge fan of the Eye Witness books.