What's the difference ?

Generally MPEG-2 HD encodes are seen when a transport stream is used as the source, since it's the standard encoding format for a TS.

H264 has a number of improvements over the MPEG standard formats, though listing them all would be an exercise in futility. It exists as a joint format with MPEG-4 part 10 as well with H.264/MPEG-4 AVC in an attempt to standardize the format. More reference frames and a better approach to quantization come to mind. H.264 is used on Bluray discs (though MPEG-2 is also used in some cases), as well as most web sourced HD videos such as those from the iTunes store. It's also the encoding format of choice for most HD encoders due to its good performance to compression ratio and advanced features.

VC-1 was a proprietary microsoft improvement to the MPEG-2/MPEG-4 part 2 standard that was used as the standard video format for the Xbox360, and was used as the one of the formats on HD DVDs before the format went defunct. It's also used on some blurays, usually in conjunction with Dobly's new "TrueHD" sound format.

Unless you have some pressing compatibility issues I wouldn't worry about it too much though :)
 
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