I rethought Clerks (and the entire 90s sample) - see below:

Here's my first cut at a top ten list by decade (will count 1959 with the 60s)

60s
1. Some Like It Hot 1959
2. Dr. Strangelove 1964
3. The Graduate 1967
4. A Shot in the Dark 1964
5. The Producers 1968
6. The Odd Couple 1968
7. The Apartment 1960
8. The Pink Panther 1964 (should have been on my initial list)
9. It's a Mad, Mad, Mad, Mad World 1963
10. Take the Money and Run 1969 (should have been on my initial list)

70s
1. Young Frankenstein 1974
2. Blazing Saddles 1974
3. M*A*S*H 1970
4. Monty Python and the Holy Grail 1975
5. Annie Hall 1977
6. National Lampoon's Animal House 1978
7. What's Up Doc 1972
8. The Sunshine Boys 1975
9. The Jerk 1979
10. Slap Shot 1977 (should have been on my initial list)
HM: Monty Python's Life of Brian 1979

80s (could not stop at 10, listed 15)
1. Airplane! 1980
2. The Naked Gun - Taken from the Files of Police Squad 1988
3. Fast Times at Ridgemont High 1982
4. Tootsie 1982
5. Raising Arizona 1987
6. This Is Spinal Tap 1984
7. Ghostbusters 1984
8. Caddyshack 1980
9. Ferris Bueller's Day Off 1986
10. History of the World: Part I 1981
11. Stripes 1981 (another one I can't believe I left off)
12. A Fish Called Wanda 1988
13. National Lampoon's Vacation 1983
14. Better Off Dead 1985
15. Planes, Trains and Automobiles 1987
HM1. Trading Places 1983
HM2: The Princess Bride 1987

90s (didn't do a good job on my original list - realize that my list needed a lot of work)
1. The Big Lebowski 1998
2. Rushmore 1998
3. Office Space 1999
4. Groundhog Day 1993
5. Lock, Stock and Two Smoking Barrels 1996
6. Clerks 1994
7. There's Something About Mary 1998
8. Austin Powers: International Man of Mystery 1997
9. Waiting for Guffman 1996
10. Robin Hood: Men in Tights 1993
HM: American Pie 1999

00s
1. Anchorman: The Legend of Ron Burgundy 2004
2. Super Troopers 2001 (can't believe I left this off the list)
3. Old School 2003
4. The 40-Year Old Virgin 2005
5. Wedding Crashers 2005
6. The Hangover 2009
7. Shaun of the Dead 2004
8. Zoolander 2001
9. Little Miss Sunshine 2006
10. Meet the Parents 2000
HM. Sideways 2004

Me, too. He is a certified genious.

Melvin Kaminsky top 10 list:

1. Young Frankenstein 1974 (top 5 favorite movie of all time)
2. Blazing Saddles 1974 (very close second)
2a Get Smart (TV Show) (favorite TV show of all time)
3. The Producers 1968
4. History of the World: Part I 1981
5. Robin Hood: Men in Tights 1993
6. Silent Movie 1976
7. Spaceballs 1987
8. High Anxiety 1977
9. Dracula: Dead and Loving It 1995
10. Life Stinks 1991
HM: The Twelve Chairs 1970 (never seen it)

Little known note: Mel Brooks is one of only ten people to have won an Academy Award, an Emmy Award, a Grammy Award and a Tony Award.