Shooting video with your iPhone horizontally with the volume buttons on the top, home button to the left actually shoots video upside down.
Apple compensates for this using Quicktime metadata to flag the video as rotated. iOS or Quicktime reads the metadata and orients the video appropriately during playback.
For any apps that don't read Quicktime metadata, the videos play upside down.
The interesting part is that Apple encourages holding the phone in the "volume buttons up" orientation, since the volume-up button can be used as a shutter fire button.
This is irritating if:
- Quicktime isn't your media player of choice
- You want to convert videos with Handbrake
- You don't use a Mac (this is your own fault)
The only fixes are to shoot your video with the volume buttons down and home button to the left, or to open each video with Quicktime 7 Pro and flip the video.