Techniques and tools for skip modes in encoding and decoding of inter-layer residual video are described. For example, an encoder encodes multiple macroblocks of a picture of inter-layer residual video. For a current macroblock that is skipped, the encoder selects a skip mode from among multiple available skip modes and uses the selected skip mode when encoding the current macroblock. The skip modes can include intra skip mode and predicted-motion skip mode. A corresponding decoder, for the current macroblock, selects and uses the skip mode for the current macroblock during decoding. As another example, an encoder encodes multiple channels of a picture of inter-layer residual video. For each channel, the encoder determines whether to skip the channel. The encoder signals channel skip information to indicate which channels are skipped. A corresponding decoder parses the channel skip information and determines on a channel-by-channel basis whether to skip the respective channels.