The rail pass is definitely the way to travel across Japan if you are going longer distances - here I very much agree with you, Duo. However, the statement you quoted from my previous posting is soley based on the OP's original itinerary stated (5 days in Tokyo - Nakano, Ikebukuro, Shibuya) - lets look at the numbers I based this suggestion on:
28,300Y - 7 day 'Ordinary' Rail Pass ticket (price from
JR Railpass prices)
6,220Y - N'EX Tickets to / from Shinjuku station (3,110Y X 2 - price from
the JR Railways Group Airport Shuttle site)
Subtracting out the price of the N'EX tickets from the cost of the Rail Pass leaves a balance of
22,080Y left that will need to be 'zeroed' out before breaking even - which means approximately 4400Y of travel via JR Trains (and buses too, but the bus system is sort of confusing from what I understand) per day for the 5 days - which is about $40 USD. Now, using my recent trip to Japan as a guide (as that's all I have to base it on) which I mentioned previously to be about $6 USD per day - but let's use $10 for easy of calculations (just for reference, we tried to travel to two neighboring locations per day - such as Ueno and Asakusa, Marinouchi and Ginza, etc), that would mean traveling nearly 4 times as much as my GF and I did per day before you would break even on the rail pass price alone.
Now, if one were going to go to Kyoto, or Osaka or other more distant destination outside of Tokyo via Shinkansen, then by all means, yes, it is definitely worth the price of the rail pass (this is what we did and the cost of the round trip tickets to Kyoto from Tokyo equals about as much as you'd pay for the 7-day rail pass). But for the short stay limited to Tokyo the OP is currently asking about, I'd have to still suggest not getting a rail pass.
I'm sorry for your bad experiences with the subways, Duo - I have nothing but raves for it from my recent trip. The subways (linked with transferring to the JR trains as needed) usually help cut travel time down for a lot of places we went to visit. The JR Yamanote train circles all the best sites aroud Japan proper, but as it goes
around Tokyo (which takes about 45 min to an hour, I believe, to loop back to your original stop), it does take a while to get to places on the 'far' side of the loop (such as going from Shinjuku to Ueno). Using the subway system in conjunction with the JR trains, it does help a lot in cutting down travel times (at least it did in my experience if you add up the travel time to and from the much further train station in my case - YMMV depending on your proximity to stations).
Truth be known, there is the Chuo local and rapid line that does cut across Tokyo as well, so you can use that as well to help save time on the JR lines. But with a much wider selection of subway lines and station locations, I think it might be better to give the subway systems a try. That is, unless you truly only plan on visiting those 3 aforementioned places (Shibuya, Ikebukuro and Nakano) - then I'd say chuck this portion of the information I'm giving you as all of those areas are directly accessible via the JR lines
The main reason I still recommend the subway is that there are usually more stops in the major districts of Tokyo which increases the chances of the subway stations being a lot closer to the any particular hotel one might be staying at (unless your hotel is very close by the rail lines, then all the better too!). Subways too have more lines and some places, you can't get by the JR trains without walking a good distance - like for example, Roppongi and Ginza are not accessible via JR lines directly, while each has at least 1 if not 2 subway lines within each district - with multiple stops within it too.
Also, bear in mind the 'rush' hours in Tokyo too - from 7 until 9 in the morning and from 7 until 9 at night - I'd avoid traveling any line (train or subway) as there is a good chance that it will be extremely packed just as Duo says (which I also found out the hard way... it's amazing how many people can be shoved into a train / subway car, isn't it - and there always seems to be room for 5 more too...). During these times, its good to go and get something to eat
Duo does bring in a good point, however - if you do only stick to the JR lines, it does make traveling much easier as you don't have to transfer from one part of the station (the subway area) to the other part of the same station (the JR portion). I must admit that the first time is a bit daunting and I must also admit that once we did get a bit turned around in Shinjuku station - but really it was our non-attention to what entrance / exit we took as we were trying to find the locker we placed our bags in on the last day we where in Japan, so it really was our fault for not paying closer attention to the big EAST EXIT sign. However, barring the above two exceptions, navigation of the stations wasn't too difficult for a non-train riders like my gf and I - we found our way with very little searching around for which direction to go in- if in doubt, follow the crowds going in
. Even if you do get lost or don't pay the right fair, don't feel too bad, as I've heard that even Japanese tourists visiting Tokyo sometimes gets turned around a bit - and they read / speak the language
and I swear, I saw more Japanese people at the fare adjustment window than tourists...
I suggest printing out and carrying with you the following two maps:
the Tokyo Subway map - this map shows you the two major subway lines (the Metro and Toei lines) and how they interconnect with the JR lines. This was by far the more useful of the two for me, as the nearest stop to the hotel was the Shinjuku Sanchome subway stop, and from there, we went all over the place.
JR Railways Tokyo map - this map gives you an overview of the JR lines to the Tokyo and outer regions. This was mainly used as a backup to the subway map as the two main JR lines (the Yamanote and the Chuo) are shown the above (just not in the right colors, see below) and to have it for my 1 known trip outside the Tokyo loop - to Nakano (as no subway line goes directly there).
The other main use for the map are the colors of the lines - as these will be the same as the colors on the trains as well as the signs that lead you to the tracks. And too, the maps also help you coordinate locations on the fare maps where you buy your train / subway tickets, just in case it's not in English (most were, but there were one or two that didn't have the station names in Romanji).
geesh, I seem to write a lot about this... hope this hasn't bored you and I hope it is helpful! And yes, please take a lot of pics of your trip!
seems like I am getting a lot of advice on taking the subway trains for the few places that I am planning to visit... I will go and get some research done and see if I can work out a list of places to visit and budget from there. Thanks guys for all these information. By the way, I am having problems booking a hotel in Shinjuku. Will be be too far away to Nakano should I book another hotel in Asakusa? The map I had printed out gives me the impression that it seems rather far.... 
). I must admit I do hate wearing a pouch as I tend to put a of of things especially change in loose coins which tends to be very heavy and making it very difficult for me to move around and I like to travel light. Perhaps a pair of jeans with lots of pockets?
