File formats naming:
"MP4" files use the Iso Base Media File Format (also "Atom/Box"), originating from QuickTime.
"JPG" files are using the "JFIF" format (=JPEG File interchange format).
"MP3" files are using a ID3 header followed by "Layer 3" (original name) streams dumps.
Older MS Office "DocFile" "OLE" files are using the CFBF "Compound File Binary Format".
Flash: SWF = "Shockwave Flash" first, then "Small Web File".
What's the original name of the "DOS MZ executable" format?

Anything else?

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@Ange
Do deflate and gzip count? They have different headers, but iirc are identical apart from that.

@robryk GZip could use another algorithm (dedicated compression method byte), Gzip files can be made of several members concatenated (see BGZip). Even Zlib uses Deflate in its own way ;)
speakerdeck.com/ange/gzip-equa

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