Short list of stores I know currently donating part or all of the proceeds from sales to Japan relief efforts! [Will be adding as I find out about more.]
This and That from Japan (who I believe is located in Japan) is donating 15% of total sales to Save The Children Japan as well! Lots of Japanese fabrics, trims, and other fun craft-related things in the shop. They're all soooo kawaii! And my experience with Japanese fabrics is that they're high quality and nice weights. :3 This donation project seems to be ongoing.
Ykonna is donating 100% of proceeds (your total purchase, minus shipping) to Save The Children, up until the end of the month. I already bought two necklaces, and she donated the money the next day (almost immediately ^^). This is a really good opportunity to snatch up her Link and epic Mario Bros. necklaces!
Steppie is giving 50% of proceeds to the Red Cross in Japan, but this ends tomorrow (Tuesday) night, Pacific time. She screens her artwork onto tees, sweaters/hoodies, and tote bags! Also some Scrabble tile rings, cards, and mugs. Ninjas and pandas, oh my! I'm a huge fan of her Panda Bums couple mug set, 8-bit "NINJA" windbreaker, and nerdy panda tank. I also own her "I'm A Ninja" charcoal hoodie and black mug :] More info here.
Amy/Shrinkle mentioned a "Pray for Japan" event in LA this Saturday, and there will be a pop-up shop for Sugarpill Cosmetics there! 100% of sales will be donated to the Japanese Red Cross as well. Her makeup has really good color payoff, so if you're in the area (or know anyone who is!), it's worth checking out, and it's for a good cause. They're also looking for volunteers for the show, so that's another way to help out! As far as I know, purchases from the Sugarpill store online don't count though.
Ann from handmadekpopgoods on Tumblr is giving people until the 18th to get in DIY charms orders. 50% of total price + shipping will be donated, and the custom charms do NOT have to be kpop members! I believe someone ordered Evanescence, Paramore, and Anberlin charms to help donate. They're super cute, and you can order them by themselves or as necklaces, key chains, rings, phone charms, car/mirror charms, or bracelets (pricing and other info). She's also known as Destination Design on Etsy, but I don't think her Etsy store will be included in a donation project. Oh! Forgot to add that everyone who participates in her donation project will also be entered in a raffle for a towel lollipop :D
Lisa of kpopbracelets, also on Tumblr, is planning on ordering a few hundred HOPE bracelets, selling for $8 each (including shipping), and 100% of proceeds will be donated. Her goal is to order and sell 325 of them, so she can donate $2000 total. They're white 1" silicone bracelets, the O in HOPE is a red circle like on the Japan flag, and the other side features the date of the earthquake as well as "Japan" in Kanji/Chinese characters. More info here. [I know Gaga is doing them too, but it bothers me that you're paying $5 for the bracelet and THEN you choose whether or not to donate on TOP of that :/]
You can also make a direct donation. I know Red Cross, Save The Children (link above), and Tzu Chi (a Taiwanese charity, the first on the scene after the earthquake struck) are legit. I think the Red Cross requires a minimum of $10? The Tzu Chi link is to the US donation page, and I get the feeling if I link the actual Taiwan one, it'll be in Chinese. So... Yeah. I've actually done service with Tzu Chi before though, and I love them.
Another way is donating through this page, which was created by the JSA (Japanese Student Association) from my alma mater, UCSD. The org's president is in contact with the governor of the Miyagi prefecture, so they're trying to get the money directly to them, in order to achieve the best allocation. (No minimum.) They're keeping the page updated with progress and where exactly the money will go.
Most, if not all, of these sellers are posting updates about how much they've raised, and some are even going to screencap the donation when they send it.
This earthquake and tsunami hit a little close to home for me, and I'm just thankful that my close family friend was back in California for their school break when it happened. I'm also glad that everyone else I know in Japan is safe and sound, and Taiwan wasn't really hit. But seriously, every little bit helps! If you can donate, please do ^^