Oh ... we got a one-liner :)

  DB<56> $_ = "AAATTTAGTTCTTAAGGCTGACATCGGTTTACGTCAGCGTTACCCCCCAAGTTAT
+TGGGGACTTT";

  DB<57> $threshold = 3;

  DB<58> x sort { length($b) <=> length($a) } grep { length >= $thresh
+old } /(A+|C+|G+|T+)/g
0  'CCCCCC'
1  'GGGG'
2  'AAA'
3  'TTT'
4  'TTT'
5  'TTT'
  DB<59>
[download]

EDIT

and for the original problem

  DB<59> x sort { length($b) <=> length($a) }  /(AA+|CC+|GG+|TT+)/g
0  'CCCCCC'
1  'GGGG'
2  'AAA'
3  'TTT'
4  'TTT'
5  'TTT'
6  'TT'
7  'TT'
8  'AA'
9  'GG'
10  'GG'
11  'TT'
12  'AA'
13  'TT'
14  'TT'
  DB<60>
[download]