Zoom H2 recorder, selecting microphone pattern and adjusting level with the built-in meter to fit the particular acoustic environment. I place the H2 as close as possible to the audio source.
I typically record WAV-48kHz-16bit. While the H2 is capable of 24bit recording, I've not found a significant difference over 16bit recording in carefully controlled tests, and 96kHz is only needed for critical mastering.
To make syncing easy, I start the camera recording, start the H2 recording, then rap the H2 with my finger. It's dead easy in post-processing to match the "thunk" of the rap in the H2 audio to the rap in the video. (I don't use camera audio for matching because of audio delay at the camera.)
When I convert for YouTube, I encode video with AAC audio at a variable bitrate of 192 Kbps.