There are no zones, just lentgh of trip
For simple trips the Metro range from 160 (2 or 3 stations) to 300 for the other side of the network
The JR lines and other provate railroad companies (Odakyu, Tobu, Seibu, a lot more) ranges from 120-130 to a few thousand yen depending on the length...
If you change between lines, you may have to add the prices, if they are two different companies.
it is not rare to pay from 500 to 1000 to go from sowhere in the vicinity of Tokyo to the other side of the capital.
You can use the website
http://www.jorudan .co.jp to find out different way and prices from different places in japan.
For the commuter passes, the math is (in my opinion) Quite simple.
First, you have a pass ONLY for the part you will be taking, if you go anywhere else, you pay like anybody else.
For example a JR pass from Ikebukuro to Shibuya lets you get off freely in Shinjuku and other station in between, but get off anywhere else and you pay the price from the nearest station on your pass.
For the price, it is roughly 30 times your normal trip, meaning, that if you take the way 10 times or more a week (morning and evening 5 days), it's a good deal, if less, you're better off paying each time.
this is for one month pass, the three or 6 months passes are a little more advantageous but, not a lot, for my pass I pay 12500 for one month and 36000 for 3...
One thing to be aware of : There is now a IC card for almost every train/metro company. (suica for JR, Pasmo for the metro and other private companies) they are compatible between network (even if you have to pay if you use two companies) and you can have your pass on it. in that case, you can take whichever way you want, using long ways, a lot of different companies, and you will pay on arrival the lowest price from the departure point to the goal... and sometimes you can spare a few hundred yens this way.
Hope that helps.