Abacus Soroban (free) - old style calculator. I did see a lady using one at a bank like 15 years ago. Not sure I'd be able to see that though anymore. Quick way to add large numbers. Top one down makes it 5 and the bottom ones instead of 1, 2, 3, 4 become 6, 7, 8, 9.

Gengou Free shows year correlating to Emperor's year. Also a paid version which has a tad more functionality (2nd and 3rd screenshots). Not sure if bank books still stamp your deposits / withdrawals with the Emperor's year in Japan.

ITmedia (free) tech news articles (RSS Feeds) in Japanese. Covers Apples, Digital Life, IT, MacWire for iPhone. Shows you number of new articles on app icon and also within index of app. Max 20 feeds per section

Spell Number (free) enables you to use emoji for email or notes or whatever. Once you do the trick 9876543.21 and enable emoji you can delete this app. Remember only fellow iphone / ipod touch users can view these emojis.

Today's AD in Japan (free) shows magazine front covers. Double tap to zoom in or out or pinch. Can do slideshow and pause. Can rotate iphone for landscape mode too.

TV Listings (free) schedule of TV shows in Japan. Let me repeat that for bumbling idiots. For those that live in Japan not wannabes. For details does use safari but allows you to stay within the app at least.

Zoome AT (free) has sections Featured, New Arrivals and Ranking. This is basically Youtube for Japanese iPhone apps / game reviews.

Other free Japanese apps
Ballo! (free) reading forums on 2ch about TV channels NHK, TBS, Fuji, etc. Landscape or portrait view. In landscape it'll scroll constantly new posts.
J-Clock Kanji Clock if you get this your weird
Katana Japanese Sword (free) same crap as light saber stuff.
Norikae (free) gives fare costs for JR and JTB.
Sankei Newspaper (free) nothing like reading the scanned in Japanese newspaper with ads and all. Can zoom twice just double tap. Long swipes left or right to navigate through the pages.
Wikiamo (free) good way to access Japanese Wikipedia on your iphone.

Some Japanese apps that cost some yen

Mindless Entertainment
iBonsai watch your little Bonsai tree grow.
iZen Garden relaxing sands and chuck stones in the sand
Koi Pond bang your head and throw up
Ninja Buddy control your ninja toss those star thingies at him.
Omikuji and Japanese Omikuji gets those buddist fortune telling papers on new years.

Pachinko
Pachinko is based on a 1976 pachinko machine.
Sho Chiku Bai Pachinko try demo is more modern pachinko version

Shogi
Kaikinoki Shogi (Japanese Chess) both look pretty decent
Shogi Z (Japanese Chess) not sure which one is better
Shogi-ban is free but has no AI just play with 2 players on same device.

Updated February 25, 2009

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