There is another site that appears to collate info about shows lower in the ratings list, probably from postings on 2channel and elsewhere by people who work for companies that have paid Video Research for the full list.
Here is a translation of the latest rankings list. The most recent ratings available are for the end of February. Some shows are not listed, and I've edited out some others that I didn't know or didn't seem of interest. Shows that are only broadcast on satellite or premium channels are not included in Video Research's totals, and do not appear on the other site, either.
The highest late-night ratings are for NANA (avg 4.4, early late-night, 11:55) and Nodame Cantabile (avg 4.4, but it has fallen from initial dizzying heights), and Death Note (avg 3.1). Next are History's Greatest Disciple Kenichi (2.5), Corda D'Oro (2.4), and Getsumen To Heiki Miina (2.3). Getsumento is a big hit in Japan, but doesn't seem as popular in Western countries.
Next come Code Geass (2.1) and Ghost Hunt and Hidamari Sketch (both 1.8) and Manabi Straight and Busou Renkin (1.7). Then there is a low group of Super Robot Wars (1.5), Tokimeki, Galaxy Railways (both 1.4), Venus vs. Virus, Red Garden (both 1.3), Master of Epic, Yamato Nadeshiko, Souten no Ken (all 1.2), and Sumomo mo Momo mo (1.1). Some shows are not included in the list.
The thing that strikes me most is the popularity of shows aimed primarily at females: NANA, Nodame, and Corda D'Oro. And we might include the prime-time show Kirarin Revolution in that. It started low but has gradually risen into the same range as Gintama, and about triple Negima's numbers.
The thing that strikes me most among shows in prime time is the dismal performance of the very good show Negima!?, which is clearly being broadcast at the wrong time: 5:30 Wednesday evenings, rather than late at night.
Oricon also has a weekly DVD sales ranking.
Here is a list of average rankings between the beginning of January and the end of February. Data is available for different numbers of episodes for different shows, and the source is unofficial, so this is a very rough guide that the exactness of the figures makes seem more accurate than it is:
|18:00 CX||Chibi Maruko-chan||14.1|
|19:30 ANB||Crayon Shin-chan||10.8|
|19:30 NTV||Detective Conan||9.7|
|19:30 TX||NARUTO Shippuden||8.0|
|19:00 TX||Pokemon Diamond and Pearl||7.8|
|08:30 ANB||Yes！Precure 5||6.7|
|18:00 ETV||MAJOR 2nd season||6.6|
|19:00 TX||Eyeshield 21||4.6|
|18:00 TX||Kirarin Revolution||4.4|
|24:45 CX||Nodame Cantabile||4.4|
|10:00 TX||Fushigiboshi Futagohime Gyu!||4.3|
|10:30 TX||Kateikyousha Hitman REBORN!||4.2|
|09:00 TX||Otogijushi Akazukin||4.2|
|08:00 TX||Deltora Quest||3.9|
|18:00 TBS||Tempou Ibun Ayakashi Ayashi||3.2|
|24:56 NTV||DEATH NOTE||3.1|
|18:30 ETV||Tsubasa Chronicles||3.1|
|24:55 TX||History's Greatest Disciple Kenichi||2.5|
|25:00 TX||Corda D'Oro||2.4|
|26:15 CX||Getsumen To Heiki Miina*||2.3|
|25:55 TBS||Code Geass||2.1|
|25.25 TBS||Hidamari Sketch||1.8|
|25:00 TX||Ghost Hunt||1.8|
|25:30 TX||Gakuen Utopia Manabi Straight||1.7|
|25:00 TX||Busou Renkin||1.7|
|07:00 TX||Demashitaa! Powerpuff Girls||1.5|
|25:30 TX||Super Robot Wars OG||1.5|
|25:30 TX||Tokimeki Memorial～Only Love～||1.4|
|26:25 TBS||Galaxy Railways~Eternity Junction~||1.4|
|25:55 TBS||Venus Versus Virus||1.3|
|26:40 ANB||RED GARDEN||1.3|
|26:30 TX||Master of Epic ～The AnimationAge～||1.2|
|25:30 TX||Yamato Nadeshiko Shichi Henge||1.2|
|26:40 ANB||Souten no Ken||1.2|
|25:35 NTV||Sasami Mamou Shoujo Club||1.1|
|26:40 ANB||Sumomo mo Momo mo||1.0|