There have only been 2 NFL Quarterback to throw for over 5000 yards in a single season, Dan Mario and now Drew Brees, who came up 15 yards short in the 2008 season. Dan Mario's NFL record has been in place since 1984. There have been 74 NFL QB's who have thrown for over 4000 yards in the NFL in a single season. Peyton Manning has thrown for over 4000 yards 9 times so far in his career. Dan Marino hit the 4000+ mark 6 times during is hall of fame career. Brett Favre has done it 5 times, and Warren Moon 4 times.

NFL All-Time Leaders	NFL Single Season Leaders
Total Passing Yards Leaders	Passing Yards Leaders
Touchdown Passes Leaders	Touchdown Passes Leaders
Rushing Yards Leaders	Rushing Yards Leaders
Receiving Yards Leaders	Rushing Touchdowns Leaders
Touchdowns (RB and WR) Leaders	Receiving Yards Leaders
	Receiving Touchdowns Leaders

Single Season NFL Passing Leaders - 4000+ passing yards
Rk	Player	Team	Yards	Year
1	Dan Marino	Miami Dolphins	5,084	1984
2	Drew Brees	New Orleans Saints	5,069	2008
3	Kurt Warner	St. Louis Rams	4,830	2001
4	Tom Brady	New England Patriots	4,806	2007
5	Dan Fouts	San Diego Chargers	4,802	1981
6	Dan Marino	Miami Dolphins	4,746	1986
7	Daunte Culpepper	Minnesota Vikings	4,717	2004
8	Dan Fouts	San Diego Chargers	4,715	1980
9	Warren Moon	Houston Oilers	4,690	1991
T10	Warren Moon	Houston Oilers	4,689	1990
T10	Rich Gannon	Oakland Raiders	4,689	2002
12	Neil Lomax	St. Louis Cardinals	4,614	1984
13	Trent Green	Kansas City Chiefs	4,591	2004
14	Kurt Warner	Arizona Cardinals	4,583	2008
15	Peyton Manning	Indianapolis Colts	4,557	2004
16	Drew Bledsoe	New England Patroits	4,555	1994
17	Jay Cutler	Denver Broncos	4,526	2008
18	Lynn Dickey	Green Bay Packers	4,458	1983
19	Dan Marino	Miami Dolphins	4,453	1994
20	Steve Beuerlein	Carolina Panthers	4,436	1999
21	Dan Marino	Miami Dolphins	4,434	1988
22	Drew Brees	New Orleans Saints	4,423	2007
23	Drew Brees	New Orleans Saints	4,418	2006
T24	Peyton Manning	Indianapolis Colts	4,413	2000
T24	Brett Favre	Green Bay Packers	4,413	1995
26	Peyton Manning	Indianapolis Colts	4,397	2006
27	Mark Brunell	Jacksonville Jaguars	4,367	1996
28	Drew Bledsoe	Buffalo Bills	4,359	2002
29	Kurt Warner	St. Louis Rams	4,353	1999
30	Bill Kenney	Kansas City Chiefs	4,348	1983
31	Scott Mitchell	Detroit Lions	4,338	1995
32	Don Majkowski	Green Bay Packers	4,318	1989
33	Jim Everett	Los Angeles Rams	4,310	1989
34	Marc Bulger	St. Louis Rams	4,301	2006
35	Jeff Garcia	San Francisco 49ers	4,278	2000
36	Peyton Manning	Indianapolis Colts	4,267	2003
37	Warren Moon	Minnesota Vikings	4,264	1994
38	Warren Moon	Minnesota Vikings	4,228	1995
39	Brett Favre	Green Bay Packers	4,212	1998
40	Tony Romo	Dallas Cowboys	4,211	2007
41	Jon Kitna	Detroit Lions	4,208	2006
42	Peyton Manning	Indianapolis Colts	4,200	2002
43	Vinny Testaverde	Baltimore Ravens	4,177	1996
44	Steve Young	San Francisco 49ers	4,170	1998
45	Elvis Grbac	Kansas City Chiefs	4,169	2000
46	Brett Favre	Green Bay Packers	4,155	2007
47	Jeff George	Atlanta Falcons	4,143	1995
48	Dan Marino	Miami Dolphins	4,137	1985
49	Peyton Manning	Indianapolis Colts	4,135	1999
50	Brian Sipe	Cleveland Browns	4,132	1980
T51	Peyton Manning	Indianapolis Colts	4,131	2001
T51	Carson Palmer	Cincinnati Bengals	4,131	2007
53	Dan Marino	Miami Dolphins	4,116	1992
54	Tom Brady	New England Patriots	4,110	2005
55	Jay Schroeder	Washington Redskins	4,109	1986
56	Brett Favre	Green Bay Packers	4,091	1999
57	Jake Plummer	Denver Broncos	4,089	2004
58	Brett Favre	Green Bay Packers	4,088	2004
59	Drew Bledsoe	New England Patriots	4,086	1996
60	Dan Fouts	San Diego Chargers	4,082	1979
61	Kerry Collins	New York Giants	4,073	2002
62	Jon Kitna	Detroit Lions	4,068	2007
63	Phil Simms	New York Giants	4,044	1984
64	Peyton Manning	Indianapolis Colts	4,040	2007
65	Trent Green	Kansas City Chiefs	4,039	2003
66	Aaron Rogers	Green Bay Packers	4,038	2008
67	Carson Palmer	Cincinnati Bengals	4,035	2006
68	John Elway	Denver Broncos	4,030	1993
69	Steve Young	San Francisco 49ers	4,023	1993
70	Trent Green	Kansas City Chiefs	4,014	2005
71	Philip Rivers	San Diego Chargers	4,009	2008
72	Joe Namath	New York Jets	4,007	1967
73	Brad Johnson	Washington Redskins	4,005	1999
74	Peyton Manning	Indianapolis Colts	4,002	2008

** Updated Jan. 8th, 2009

Sources:
pro-football-reference.com
databasefootball.com
wikipedia.org
espn.com