perl -l054p012e'($\,$a)=($a||$\,$b||$/);$b=$\'
[download]

:-)

Update:

$ perl -l054p012e'($\,$a)=($a||$\,$b||$/);$b=$\' <<EOT
> a
> b
> c
> d
> e
> f
> g
> h
> EOT
a,b
c,d
e,f
g,h

Makeshifts last the longest.

My attempt,

perl -pe '$_=/\S/?do{chop;$_.",".<>}:""'
[download]

assumes non-blank lines come in pairs.

Yours doesn't look right to me though...

286,0 sauoq@grover:~$ perl -l054p012e'($\,$a)=($a||$\,$b||$/);$b=$\' <
+ test.txt
a,b
,c
d,287,0 sauoq@grover:~$ cat test.txt
a
b

c
d
288,0 sauoq@grover:~$
[download]

-sauoq
"My two cents aren't worth a dime.";

It ignores the issues of blank lines, if you mean that, but so does the OP's code because next doesn't work the way he thinks. (The print is in a continue block so it always gets executed short of dieing.) I chose to note and ignore it. What I was trying to do is achieve the described behaviour without explicitly manipulating $_ or printing anything myself.

Makeshifts last the longest.

Not for big files

C:\test>type junk
A
B


C

D

C:\test>perl -0pe"y/\n//s;s/(.+)\n(.+)/$1,$2/g" junk
A,B
C,D
[download]

perl -pe 'goto LINE unless /\S/; s/\n/,/ if ($a = 1 - $a)'
[download]

--
integral, resident of freenode's #perl

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/?--$|&&s/\n/,/:($_="")'
[download]

-sauoq
"My two cents aren't worth a dime.";