perl -ne 'chomp;for(split /,/){print ++$i%3 ? "$_," : "$_\n" }'

There are some corner cases where the different solutions disagree.

The test file:

a,b,c,d,e
f,g,e,h
i,j,
l,m
n
,
[download]

greatshots' output:

a,b,c
d,e,f,g,e
h,i,j,l,m,n,
[download]

(no newline at the end)

My output:

a,b,c
d,e,f
g,e,h
i,j,l
m,n,
[download]

(no trailing newline)

ikegami's output:

a,b,c
d,e
f,g
e,h
i,j

l,m
n
,
[download]

It would be interesting to know what the desired output is (and if it matters at all)

Treat "," as the end of line marker (-054).
Every third line ($. % 3 == 0),
change the trailing comma to a newline (s/,/\n/).
Print the result (-p).

perl -054pe"$.%3||s/,/\n/"
[download]

In action:

>echo a,b,c,d,e,f,g,h,i | perl -054pe"$.%3||s/,/\n/"
a,b,c
d,e,f
g,h,i
[download]

Update: As moritz points out, I assumed all the input is on one line.

while ( <DATA> )
 {
   chomp;
   my @line = ($_ =~ /\w+,\w+,\w+/g) ;
   printf "%s\n",  join("\n",@line);
 }
[download]

perl -F, -lane'print join ",", @x while @x = splice @F, 0, 3'
[download]

#!/usr/bin/perl

use warnings;
use strict;

while (<DATA>) {
    chomp;
    my @line = split /,/;
    while (my @excerpt = splice(@line, 0, 3)) {
        print join(",", @excerpt), "\n";
    }
}
 
__DATA__
userid,application_id,time,userid,application_id,time,userid,applicati
+on_id,tim
userid,application
,
[download]

Hi greatshots,

This may be useful for you

while (my $line = <DATA>){
    my $i=0;
    chomp($line);
    my @array = split(',',$line);
    while($i<=$#array){
        print "$array[$i+2]\n";
        $i++;
    }
}
[download]

Punitha