Which IC Card?

I will be in Japan for 16 days and will have a JR Pass. My main base cities where I will be staying are Osaka, Kyoto and Tokyo. I will take day trips to Yokohama, Himeji, Okayama, Nagoya, Inuyama, Nagano, Kanazawa, Gifu and Yoshino.

Which IC card should I get when I first arrive in Osaka? Thanks

ICOCA is the card sold in Osaka: you will need to buy that.
And thats a good thing, as ICOCA is the most widely used, eg for Himeji, Hiroshima and Miyajima
http://www.japan-guide.com/e/e2359_003.html
You will not be able to redeem the 500\ deposit in Tokyo: but in reality, 500\ is not a lot to sacrifice for the convenience.

And thats a good thing, as ICOCA is the most widely used, eg for Himeji, Hiroshima and Miyajima

Icoca is the most widely used in Western Japan. In Eastern Japan, it's Suica/Pasmo.

looking at the OP�fs itinerary ICOCA will be beneficial.

If you arrive in Osaka, your only choice is Icoca. None of the other prepaid IC cards is sold in the Osaka region.

There is almost no difference between Icoca and the other major IC cards. They have generally all the same coverage area with just a few minor exceptions. Some of these minor exceptions will work in your favor, as Okayama trams and Himeji buses happen to accept only Icoca cards but not the others.