If you read Massey's stuff you'll find that he, like Sagarin, thinks that ratings considering margin of victory are more accurate than ratings that do not. In that regard, you can get the FCS teams ranked according to his "Margin of Victory" system by going to http://www.masseyratings.com/rate.php?lg=cf , clicking on the "FCS" button, then clicking on "MOV" at the top of that column in the table.

Here are the top 25 teams:

1 Richmond 13 3 CAA
2 James Madison 12 2 CAA
3 Montana 14 2 Big Sky
4 Villanova 10 3 CAA
5 Weber St 10 4 Big Sky
6 New Hampshire 10 3 CAA
7 Northern Iowa 12 3 MVFC
8 Cal Poly SLO 8 3 GWFC
9 Appalachian St 11 3 SC
10 William & Mary 7 4 CAA
11 Wofford 9 3 SC
12 E Washington 6 5 Big Sky
13 Harvard 9 1 Ivy
14 Maine 8 5 CAA
15 S Illinois 9 3 MVFC
16 Massachusetts 7 5 CAA
17 Cent Arkansas 10 2 SLC
18 Montana St 7 5 Big Sky
19 S Dakota St 7 5 MVFC
20 McNeese St 7 4 SLC
21 N Arizona 6 5 Big Sky
22 Elon 8 4 SC
23 Liberty 10 2 BSC
24 Holy Cross 7 4 PL
25 Grambling 11 2 SWAC

Conference rankings (average strength of teams). I think this is based on the ratings that do not consider margin of victory.

Rk Conf Tms W L Rating Parity
1 Colonial 12 34 20 1.098 0.5079
2 Big Sky 9 18 18 0.921 0.5285
3 Southern 9 19 17 0.843 0.5161
4 Southland 8 20 15 0.817 0.7343
5 Great West 5 21 18 0.734 0.7046
6 Missouri Valley 9 15 20 0.631 0.5105
7 Big South 7 21 20 0.535 0.7408
8 Patriot League 7 20 17 0.485 0.5997
9 NCAA 125 98 33 0.479 0.4772
9 Div I 125 88 15 0.479 0.4772
9 FCS 125 90 100 0.479 0.4772
12 Ivy League 8 10 14 0.466 0.5571
13 OH Valley 9 15 19 0.457 0.6625
14 Mid-Eastern AC 10 11 15 0.159 0.5605
15 Northeast 8 14 18 0.073 0.4609
16 Southwestern AC 10 12 22 0.035 0.5536
17 Pioneer 9 17 14 -0.179 0.5434
18 1-AA Independents 5 19 29 -0.188 0.6774

An explanation can be found at http://www.masseyratings.com/theory/massey.htm .