my @oldlist = map {chomp; $_} <DATA>;

my @sorted = map {$_->[2] . " " . $_->[1]}
             sort {($a->[0] cmp $b->[0]) || 
                   ($a->[2] cmp $b->[2]) || 
                   ($b->[1] cmp $a->[1])}
             map { [split] } @oldlist;

#print join "\n", @sorted,"\n";

my @newlist = map {shift(@oldlist) . ' ' . $_} @sorted;
print (join ("\t", split),"\n") for @newlist;
__DATA__
a1 p1 qX5
a1 p1 q6
a1 p2 q4
a2 p3 q9
a2 p2 q8
a2 p2 q9

_OUTPUT__
a1	p1	qX5	q4	p2
a1	p1	q6	q6	p1
a1	p2	q4	qX5	p1
a2	p3	q9	q8	p2
a2	p2	q8	q9	p3
a2	p2	q9	q9	p2