Below is the national all-time win list. Got sent this information from http://www.footballfridaynight.com. 

	School	State	Record	Win%
1	Valdosta	GA	869-205-34	79.96
2	HIGHLANDS	KY	828-212-26	78.89
3	LOUISVILLE MALE TRADITIONAL	KY	815-313-49	71.33
4	MASSILLON WASHINGTON	OH	810-246-35	75.85
5	MOUNT CARMEL AREA	PA	801-290-57	72.26
6	MAYFIELD	KY	791-248-32	75.35
7	CANTON MCKINLEY	OH	785-329-42	69.72
8	EASTON AREA HS	PA	780-333-52	69.18
9	LITTLE ROCK CENTRAL	AR	778-322-48	69.86
10	HAMPTON	VA	777-250-45	74.58

As for CT schools through 2011: (records provided by the Connecticut Sports Writers Alliance football record book):

MOST WINS
School Wins Years
New Britain 739 1892-2010
Ansonia 731 1900-2010
Hillhouse-New Haven 590 1885-2010
Derby  508 1902-2010
Southington/Lewis 505 1932-2010
Shelton 478 1904-2010
New Canaan 473 1928-2010
Torrington 460 1894-2010
Berlin 4061936-2010
Weaver-Hartford 386 1924-2010