Comment Ecch (Score 1) 259
It's pretty bad out there for organization and storage. I tried using just flat directories by date as others mentioned but then it became difficult to find things when you didn't know when the event happened. Then I went with Gallery, but it got comment spammed. Then I went with Gallery 2, but that POS is a total disaster, enough that the entire project seems to be shut down.
I'm using smugmug now. Easy to upload and download, they have a fairly open API for writing your own interface, and you can easily change protection on items you upload so they're public, private, or public if you know the URL. Costs a bit of money but integrates with my EyeFi cards nicely so I don't have to worry about uploading photos at the end of the day.