Now that I've actually tested the code, I have a bugfix for it:
You should test before submitting a snippet.
Even this version has a quirk you should be aware of. It will substitute a comma for a newline on the last line of the file if the input has an odd number of non-blank lines.
You can use $a ^= 1 as a sufficiently clear alternative to $a = 1 - $a.
Golfed: perl -pe 'goto LINE if!/\S/;--$|&&s/\n/,/'
Update: Another several strokes shaved:
perl -pe '/\S/?--$|&&s/\n/,/:($_="")'
-sauoq
"My two cents aren't worth a dime.";
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