Use Black Point Compensation: this should be kept checked. Black Point Compensation ensures that the darkest neutrals of the source color space are mapped to the darkest neutrals of the destination color space. In most circumstances toggling BPC ON or OFF will result in no obvious change to the document appearance, but in some situations converted documents will look/print horrible if BPC is Off, so be very careful with this setting.
Use Dither (8-bit/channel images): as with Black Point Compensation this should be kept checked. The description box at the bottom of the Color Settings dialog box will give you some clue as to what it does.
Compensate for Scene-referred Profiles: This is a new option introduced with CS5. It compares video contrast when converting from scene to output profiles. This option reflects default color management in After Effects, and is of no real significance to Photographers.