[linux] Fastest way of finding differences between two files in unix?

You could try..

comm -13 <(sort file1) <(sort file2) > file3

or

grep -Fxvf file1 file2 > file3

or

diff file1 file2 | grep "<" | sed 's/^<//g'  > file3

or

join -v 2 <(sort file1) <(sort file2) > file3

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