Rockin' Android, based in Los Angeles, has already released The Acceleration of Suguri (a one-on-one shooter very similar to Senko no Ronde), QLIONE, and Flying Red Barrel, while the shooter Gundemonium is due out in May. They're nice packages, especially for Suguri and Gundemonium, which contains all of the current sequels and upgrades to them on a single disc, making it much easier than tracking down separate Japanese releases. You can buy physical copies from their store, or download them through Gamersgate or Direct2Drive. The physical release of Suguri is actually quite nice, as it comes in a DVD-style case and contains soundtracks for both games in MP3 format, as well as a printed manual. Considering any of the doujin games I've ever bought rarely even include an installation card, it's a nice deal for $20.
DHM Interactive is a French company that specializes in localizing niche stuff, similar to Atlus. They're bringing over the Ys DS releases (separately, for some reason, instead of the combined version released in the US) but they've also licensed Chantelise and Gunners Heart (also check out the articles for Chantelise and Gunners Heart. For right now, they only seem to offer physical copies, and at 20 euros each, it's a bit pricey for US gamers, working to about $30 each before shipping. (The same company is also releasing a Sengoku Anthology, compiling the trilogy of Neo Geo fighters, but it doesn't seem to have been released in Japan or anywhere else.)
Hopefully these legit releases will gain some traction so we see more of them and maybe one day we'll see the "bigger" names like Touhou or Melty Blood get localized. Due to their somewhat copyright infringing nature, though, it's unlikely that the ones based off other video games and manga (or any of the number of gal games) will ever get localized. (Still, Gunners Heart is based off of Skygunner, so there's always a chance.) I think the biggest obstacle, though, is that the audience for doujin gaming generally coincides with the freeloading anime audience, who most just resort to torrents, which is why the anime DVD market is as dismal as it is. So, if these interest you, these projects are definitely worth supporting.