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If you're asking about which format to download from sites that have multiple formats, I would first see if the site favors one format over another, because that would likely be their "original" format and all others are converted from that.
If not, then I would recommend epub just slightly over mobi, simply because there are more epub-only plugins for Calibre than mobi-only plugins, and you may decide you want to use these in the future.
Other than that, the two formats are pretty much interchangeable in Calibre and converting between the two is usually not a problem, so either one is fine.
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