Here are some details about the links I have on the right of the screen regarding watching games.
Justin.tv is a site I read about on other blogs, mainly npbtracker.com, and the first place I was able to watch a NPB game online. It was my go-to last year for the NPB playoffs and the Japan Series. Justin.tv is a site that allows people to post live video feeds. Often people who put on the live video also save these videos so that they can be accessed later. Games can be watched as full-screen on this site and generally have good picture quality.
Keyhole TV requires you to download a viewer. Once you have done the download, it allows you to watch live Japanese TV or listen to live Japanese radio. I believe the channels, like Justin.tv, are provided by individuals. But instead of showing whatever the individual wants to show, Keyhole TV shows the same channel or station 24/7, so you can watch NHK or Fuji TV for example anytime you want to. The main negative of Keyhole TV (as you could guess from the name) is that the screen is only about 4" x 4" in size and the picture quality in often not that good. Another negative is that it shows the main network broadcasts of games, which are normally scheduled over a two hour window, starting in the second or third inning and ending somewhere between the seventh and the end of the game depending on the speed of play. It's nice to know that Keyhole TV is there if you just want to tune in for a couple innings on a random weekend, but Justin.TV is a better option for playoff games that you know someone will be showing on there.
Last year on TBS's (the Japanese TV station that at that time owned the BayStars) website they had a page that had recordings of BayStar home games. It is a great page that allows you to watch a recording of any game from their season by top or bottom of each inning. You can either hide the score and be in suspense or turn the scores on and watch only the scoring innings. The quality is good and any game is on demand, the only negative is that every game features the last-place BayStars It provided a good place to see the Dragons when they went to Yokohama and I could watch on my terms the day after. The site is still active in spite of the BayStars' ownership change. It would be great if they were to continue this site for 2012, but that seems very unlikely.
There are many other places out there I'm sure and I hope to find some more for the upcoming year. Yahoo.jp shows Pacific League games for a fee, but I don't know that it can be viewed outside of Japan. If anyone out there knows of some other good places to watch, please don't be afraid to share.