Almost everywhere in Tokyo has a 'table charge' now. You will have to buy some small dish that is usually specific to the bar / izakaya whether you want it or not. The 'free' nibbles are what you are paying something like a fiver for for the luxury of a seat.
Most izakaya are eating and drinking places, might seem a bit odd to english people at first, but I think I prefer it now. It makes much more sense, and the prices are usually pretty good really.
There's also the "stand up" bars which are traditional and you might find stools at the bar. It's either spit & sawdust or jukebox videos etc - you chose your drink from a machine inside, put the coins in - it issues you a ticket and you give that to the barman and he serves the drink.
There are some great and crazy standup bars in Koenji, super friendly. Small stand up bars tend not to have a table charge.
Ooh and try some street drinking places. Grab some yakitori and nihonshu (sake to you and I).
Check out piss alley in shinjuku.