Over on the Handbrake forums a contributor has released an interesting tool called Muxo that allows adding soft subtitles to MP4 that are supported on the iPhone. Soft subtitles are those that can be turned on and off, rather than being actually encoded into the video with tools we've mentioned before like Submerge and RoadMovie. Entropic designed Muxo as an accessory to Handbrake, allowing you to add SRT subtitles to a fresh DVD rip. Once you load them on your iPhone you'll get a menu button that lets you turn the subtitles on and off.
Muxio is a free download here (download link).