shell replace cr\lf by comma

With sed, you could use:

sed -e 'H;${x;s/\n/,/g;s/^,//;p;};d'

The H appends the pattern space to the hold space (saving the current line in the hold space). The ${...} surrounds actions that apply to the last line only. Those actions are: x swap hold and pattern space; s/\n/,/g substitute embedded newlines with commas; s/^,// delete the leading comma (there's a newline at the start of the hold space); and p print. The d deletes the pattern space - no printing.

You could also use, therefore:

sed -n -e 'H;${x;s/\n/,/g;s/^,//;p;}'

The -n suppresses default printing so the final d is no longer needed.

This solution assumes that the CRLF line endings are the local native line ending (so you are working on DOS) and that sed will therefore generate the local native line ending in the print operation. If you have DOS-format input but want Unix-format (LF only) output, then you have to work a bit harder - but you also need to stipulate this explicitly in the question.

It worked OK for me on MacOS X 10.6.5 with the numbers 1..5, and 1..50, and 1..5000 (23,893 characters in the single line of output); I'm not sure that I'd want to push it any harder than that.

In response to @Jonathan's comment to @eumiro's answer:

tr -s '\r\n' ',' < input.txt | sed -e 's/,$/\n/' > output.txt

Try this:

tr '\n' ',' < input.txt > output.txt