Actually don't even both wasting your time converting. Download something like AvPLayerHD and just drag the files over. It will play them directly.
CineXPlayer is the best of the bunch, especially now that it's the only video app in the AppStore that supports AC3 and Dolby Digital audio.
You should still convert the videos to a natively compatible format, however, as that's the only way to get hardware acceleration. Otherwise the video player has to decode in software, which is MUCH MUCH worse on battery life. Whenever you see benchmarks showing a phone/tablet has 10+ hours of battery life with a video playing in a loop, it's because of the hardware acceleration.
Considering this, and considering how important your phone battery not being dead typically is, I highly recommend converting.