The city is full of small and medium size concert halls. These are called "live houses" in Japanese. Concerts in Tokyo start early — usually between 7 and 8 pm and often wrap up by 10pm. They generally run according to the announced schedule. This gives people time to make it home before their last train. Many concert goers have a 2nd party after a show at a nearby izakaya, eatery or bar.
In addition to live houses there are plenty of genre specific venues in the city including punk, hip hop and jazz clubs. If you're in town it's recommended to check out a show — even if it's a random band you've never heard of. Most small shows cost 2000 - 3500 yen and might feature 2-4 bands.
Tokyo's concert venues number in the hundreds. They're spread over at least 30 neighborhoods. These areas have the city's most active music scenes:
1. ShibuyaShibuya is known for hip hop, electronic dance music, pop and rock. Most of the venues in Shibuya are in an area known as love hotel hill. Several of the clubs in the area are nothing short of legendary. These include Vuenos (hip hop), Club Asia (electronic), O-nest and Quattro.
2. ShinjukuShinjuku (particularly Kabukicho) is a music lovers paradise. It's filled with small and medium sized live houses, punk bars and jazz clubs. Be warned that Kabukicho is the strangest neighborhood in Japan (it's also a little dangerous). Many of the venues in the area are "dive houses" — a live house that's a dive bar. Several are rock legends (e.g. Marz Shinjuku).
3. ShimokitazawaShimokitazawa is a hipster neighborhood that's filled with live houses and rental recording studios. Half the residents of the area are musicians. It's indie all the way in Shimokitazawa.
4. KoenjiKoenji has a similar scene to Shimokitazawa. It's a hipster neighborhood with plenty of resident musicians. Koenji has loads of small indie live houses.
5. Harajuku / YoyogiHarauku and Yoyogi are two youth-oriented neighbourhoods (beside each other). Both neighborhoods have a few well known live houses.
Yoyogi Park is a large park in the area that draws fair-weather performances (especially weekends). It's rumored that police in the park are tolerant when it comes to public event licenses. Concerts small and large, scheduled and unscheduled are a regular occurrence in the park.