This has got to be well within the top three questions I've received over the years. The three links below are just the tip of the iceburg compared to what I've recieved via e-mail since 1995.
Basicly, jerseys and caps can be found at the YakyuShop. While I have no affiliation with the YakyuShop, the person who started it has simply been a sanity saver for me. Until this was formed, there was nowhere for anyone outside of Japan to order Pro Yakyu goods as the few on-line retailers at the time refused to ship overseas. Until the YakyuShop opened, it broke my heart to tell people that there was nothing I could do to help them get Pro Yakyu goods.
Baseball cards (and a great wealth of other historical information) can be found at RobsJapaneseCards.com. Rob also has available a book he wrote, "Remembering Japanese Baseball" which I would highly recommend. I'm anxiously awaiting a sequel.
All of the above sites are in English. If you can read and type in Japanese, pretty much all of the teams' official sites sell goods, but not all of them ship overseas. You'll need to look into that on your own.
If you know of any other English languages Pro Yakyu merchandisers, please post a comment to this thread.