as a visitor to japan, getting a temp. cell phone seemed ridiculously hard. there are no prepaid SIMs/phones; you can only do a rental. and no matter what plan you get, outgoing calls will be ~90yen/minute.
so: after two days in tokyo, i wound up renting an iphone (3GS), and it was immensely helpful. having maps + gps was really fantastic. i installed and used skype pretty often - it breaks up a lot over 3G, but again, it's far better than paying 90yen/minute. i highly recommend this company: http://jcrcorp.com. i have no association with them, but they were a pleasure to work with. (also note: an android phone may work better, as iphones are on softbank which is a newer and less well established carrier).
i also found that free wi-fi seemed to be very, very rare. you can find some coffee shops with wi-fi, but you have to buy a ticket at a nearby FamilyMart for ~500yen/day.
do you know any of the language? if the answer is no, it's probably too late now; but i found that using the japanese keyboard on iphone (just kana) was very helpful to mapping stuff out.
it's worth spending a few minutes to understand the addressing system: http://en.wikipedia.org/wiki/Japanese_addressing_system. there are no street names, and it's generally very different from the US.
finally, i assume you already know this, but tokyo is not cheap; be prepared to spend a lot of money, and enjoy yourself.
feel free to contact me off-list.