Okay I'm letting all you guys do my dirty work for me, I don't want to waste my time and go through every DVD on Criterion's website, but...

what, as I stated in my title, discs include short films:

off hand I know that there are three on the Ratcatcher disc
one from off of My Life as A Dog

what else?

'Knife in the Water' has 9 of the 10 early Polanski shorts (or is it 8 of the 9?)

The Stan Brakhage disc is all shorts (I forget the name off-hand), as, I suppose, is the Beastie Boys Video Anthology.

Slacker includes Linklater's first film (although it's longer than the feature).

Quite a few, but some off the top of my head:

Eyes Without A Face -- Blood Of the Beasts
M -- M le Maudit
The 400 Blows -- Antoine and Colette

Videodrome includes Camera
And the upcoming Tout Va Bien has Letter To Jane, which I think is a short.

Here's a list Tribe over at criterionforum.org has compiled. Doesn't include the titles of the discs that the films are on, though.

Accidentally (Woo, 1968) (Spine #9)
The Act of Seeing With One's Own Eyes (Brakhage, 1971) (Spine #184)
All Boys Are Called Patrick (Godard, 1957) (Spine #238)
Angst isst Seele auf (Noshir, 2002) (Spine #198)
Antoine and Colette (Truffaut, 1962) (Spine #5)
Armageddon (Anderson, 1999) (Spine #65)
The Barber Shop (Ripley, 1933) (Spine #79)
Black Ice (Brakhage, 1994) (Spine #184)
Blood of the Beasts (Franju, 1949) (Spine #260)
Bezhin Meadow (Eisenstein, 1937) (Spine #87)
Break Up the Dance (Polanski, 1957) (Spine #215)
Camera (Cronenberg, 2000) (Spine #248)
Cat's Cradle (Brakhage, 1959) (Spine #184)
Commingled Containers (Brakhage, 1997) (Spine #184)
La Cotta (Olmi, 1967) (Spine #194)
Cours du Soir (Ribowski, 1967) (Spine #112)
Crack Glass Eulogy (Brakhage, 1992) (Spine #184)
The Dante Quartet (Brakhage, 1987) (Spine #184)
The Dark Tower (Brakhage, 1999) (Spine #184)
A Day With the Boys (Gulager, 1969) (Spine #152)
Daybreak Express (Pennebaker, 1953) (Spine #154)
Delicacies of Molten Horror Synapse (Brakhage, 1991) (Spine #184)
The Dentist (Pearce, 1932) (Spine #79)
Desistfilm (Brakhage, 1954) (Spine #184)
Dog Star Man: Part I (Brakhage, 1962) (Spine #184)
Dog Star Man: Part II (Brakhage, 1963) (Spine #184)
Dog Star Man: Part III (Brakhage, 1963) (Spine #184)
Dog Star Man: Part IV (Brakhage, 1964) (Spine #184)
L'ecole des facteurs (Tati, 1947) (Spine #111)
Entr'acte (Clair, 1924) (Spine #160)
Eye Myth (Brakhage, 1967) (Spine #184)
The Fat and the Lean (Polanski, 1961) (Spine #215)
The Fatal Glass of Beer (Bruckman, 1933) (Spine #79)
Fellini: A Director's Notebook (Fellini, 1969) (Spine #140)
Les fiances du Pont Mac Donald (Varda, 19 ) (Spine #174)
Das fidele Gefangnis (Lubitsch, 1917) (Spine #170)
For Marilyn (Brakhage, 1992) (Spine #184)
The Garden of Earthly Delights (Brakhage, 1981) (Spine #184)
Gasman (Ramsay, 1998) (Spine #162)
The Golf Specialist (Brise, 1930) (Spine #79)
Glaze of Cathexis (Brakhage, 1990) (Spine #184)
Hua Yang de Nian Hua (Kar-Wai, 2000) (Spine #147)
I...Dreaming (Brakhage, 1988) (Spine #184)
It's Impossible to Learn to Plow by Reading Books (Linklater, 1988) (Spine #247)
Kill the Day (Ramsay, 1997) (Spine #162)
The Killers (Tarkovsly, 1958) (Spine #176)
Kindering (Brakhage, 1987) (Spine #184)
The Lamp (Polanski, 1959) (Spine #215)
Letter to Jane (Goard & Gorin, 1972) (Spine #275)
Lovesong (Brakhage, 2001) (Spine #184)
M le maudit (Chabrol, 1982) (Spine #30)
Mammals (Polanski, 1962) (Spine #215)
Les Mistons (Truffaut, 1958) (Spine #185)
Mothlight (Brakhage, 1963) (Spine #184)
Murder (Polanski, 1957) (Spine #215)
Nightmusic (Brakhage, 1986) (Spine #184)
No C-4 for Daniel-Daniel (Belvaux, Bonzel, Poelvoorde, 1987) (Spine #165)
Out of Sight (Anderson, 1999) (Spine #65)
Paris qui dort (Clair, 1925) (Spine #161)
The Pharmacist (Ripley, 1933) (Spine #79)
Physical Pinball (Green, 2002) (Spine #152)
Pleasant Grove (Green, 2002) (Spine #152)
Pool Sharks (Middleton, 1915) (Spine #79)
Prelude: Dog Star Man (Brakhage, 1962) (Spine #184)
Rage Net (Brakhage, 1988) (Spine #184)
Shall We go to Your Place or My Place or Each Go Home Alone? (Halstrom, 1973) (Spine #178)
La ricotta (Pasolini, 1963) (Spine #236)
Small Deaths (Ramsay, 1996) (Spine #162)
Soigne ton gauche (Clement, 1936) (Spine #110)
The Stars Are Beautiful (Brakhage, 1974) (Spine #184)
Stellar (Brakhage, 1993) (Spine #184)
Study in color and Black and White (Brakhage, 1993) (Spine #184)
Teeth Smile (Polanski, 1957) (Spine #215)
The Truman Show (Anderson, 1999) (Spine #65)
Two Men and a Wardrobe (Polanski, 1958) (Spine #215)
Villa Santo Sospir (Cocteau, 1952) (Spine #69)
When Angels Fall (Polanski, 1959) (Spine #215)
Wedlock House: An Intercourse (Brakhage, 1959) (Spine #184)
Window Water Baby Moving (Brakhage, 1962) (Spine #184)
The Wold Shadow (Brakhage, 1972) (Spine #184)
Woodshock (Linklater, 1985) (Spine #247)

loaded

I had no idea there were that many.

Thanks for the comprehensive list... now I have figure out the disc by the director and/or spine #

Assuming those numbers are right...

Accidentally (Woo, 1968) (Spine #9) HARD BOILED
All Boys Are Called Patrick (Godard, 1957) (Spine #238) A WOMAN IS A WOMAN
Angst isst Seele auf (Noshir, 2002) (Spine #198) ALI: FEAR EATS THE SOUL
Antoine and Colette (Truffaut, 1962) (Spine #5) THE 400 BLOWS
Blood of the Beasts (Franju, 1949) (Spine #260) EYES WITHOUT A FACE
Bezhin Meadow (Eisenstein, 1937) (Spine #87) ALEXANDER NEVSKY
Camera (Cronenberg, 2000) (Spine #248) VIDEODROME
La Cotta (Olmi, 1967) (Spine #194) IL POSTO
Cours du Soir (Ribowski, 1967) (Spine #112) PLAYTIME
A Day With the Boys (Gulager, 1969) (Spine #152) GEORGE WASHINGTON
Daybreak Express (Pennebaker, 1953) (Spine #154) THE HORSE'S MOUTH [this short was originally shown in front of 'Horse's Mouth']
L'ecole des facteurs (Tati, 1947) (Spine #111) MON ONCLE
Entr'acte (Clair, 1924) (Spine #160) A NOUS LA LIBERTE
Fellini: A Director's Notebook (Fellini, 1969) (Spine #140) 8 1/2
Les fiances du Pont Mac Donald (Varda, 19 ) (Spine #174) BAND OF OUTSIDERS
Das fidele Gefangnis (Lubitsch, 1917) (Spine #170) TROUBLE IN PARADISE
Gasman (Ramsay, 1998) (Spine #162) RATCATCHER
Hua Yang de Nian Hua (Kar-Wai, 2000) (Spine #147) IN THE MOOD FOR LOVE
It's Impossible to Learn to Plow by Reading Books (Linklater, 1988) (Spine #247) SLACKER not really a short...
Kill the Day (Ramsay, 1997) (Spine #162) RATCATCHER
The Killers (Tarkovsly, 1958) (Spine #176) THE KILLERS/THE KILLERS
Letter to Jane (Goard & Gorin, 1972) (Spine #275) TOUT VA BIEN
M le maudit (Chabrol, 1982) (Spine #30) M
Les Mistons (Truffaut, 1958) (Spine #185) ANTOINE DOINEL BOX
No C-4 for Daniel-Daniel (Belvaux, Bonzel, Poelvoorde, 1987) (Spine #165) MAN BITES DOG
Paris qui dort (Clair, 1925) (Spine #161) UNDER THE ROOFS OF PARIS
Physical Pinball (Green, 2002) (Spine #152) GEORGE WASHINGTON
Pleasant Grove (Green, 2002) (Spine #152) GEORGE WASHINGTON
Shall We go to Your Place or My Place or Each Go Home Alone? (Halstrom, 1973) (Spine #178) MY LIFE AS A DOG
La ricotta (Pasolini, 1963) (Spine #236) MAMMA ROMA
Small Deaths (Ramsay, 1996) (Spine #162) RATCATCHER
Soigne ton gauche (Clement, 1936) (Spine #110) M. HULOT'S HOLIDAY
Villa Santo Sospir (Cocteau, 1952) (Spine #69) TESTAMENT OF ORPHEUS
Woodshock (Linklater, 1985) (Spine #247) SLACKER

SIX SHORTS WITH W.C. FIELDS
The Barber Shop (Ripley, 1933) (Spine #79)
The Dentist (Pearce, 1932) (Spine #79)
The Fatal Glass of Beer (Bruckman, 1933) (Spine #79)
The Golf Specialist (Brise, 1930) (Spine #79)
The Pharmacist (Ripley, 1933) (Spine #79)
Pool Sharks (Middleton, 1915) (Spine #79)

RUSHMORE: [These are three shorts Wes Anderson shot for MTV, the conceit of which is that Max Fischer is adapting these films]
Armageddon (Anderson, 1999) (Spine #65)
Out of Sight (Anderson, 1999) (Spine #65)
The Truman Show (Anderson, 1999) (Spine #65)

KNIFE IN THE WATER:
Break Up the Dance (Polanski, 1957) (Spine #215)
The Fat and the Lean (Polanski, 1961) (Spine #215)
The Lamp (Polanski, 1959) (Spine #215)
Mammals (Polanski, 1962) (Spine #215)
Murder (Polanski, 1957) (Spine #215)
Teeth Smile (Polanski, 1957) (Spine #215)
Two Men and a Wardrobe (Polanski, 1958) (Spine #215)
When Angels Fall (Polanski, 1959) (Spine #215)
[the one it's missing is his first short, 'Bicycle', from 1955]

BY BRAKHAGE:
The Act of Seeing With One's Own Eyes (Brakhage, 1971) (Spine #184)
Black Ice (Brakhage, 1994) (Spine #184)
Cat's Cradle (Brakhage, 1959) (Spine #184)
Commingled Containers (Brakhage, 1997) (Spine #184)
Crack Glass Eulogy (Brakhage, 1992) (Spine #184)
The Dante Quartet (Brakhage, 1987) (Spine #184)
The Dark Tower (Brakhage, 1999) (Spine #184)
Delicacies of Molten Horror Synapse (Brakhage, 1991) (Spine #184)
Desistfilm (Brakhage, 1954) (Spine #184)
Dog Star Man: Part I (Brakhage, 1962) (Spine #184)
Dog Star Man: Part II (Brakhage, 1963) (Spine #184)
Dog Star Man: Part III (Brakhage, 1963) (Spine #184)
Dog Star Man: Part IV (Brakhage, 1964) (Spine #184)
Eye Myth (Brakhage, 1967) (Spine #184)
For Marilyn (Brakhage, 1992) (Spine #184)
The Garden of Earthly Delights (Brakhage, 1981) (Spine #184)
Glaze of Cathexis (Brakhage, 1990) (Spine #184)
I...Dreaming (Brakhage, 1988) (Spine #184)
Lovesong (Brakhage, 2001) (Spine #184)
Kindering (Brakhage, 1987) (Spine #184)
Mothlight (Brakhage, 1963) (Spine #184)
Nightmusic (Brakhage, 1986) (Spine #184)
Prelude: Dog Star Man (Brakhage, 1962) (Spine #184)
Rage Net (Brakhage, 1988) (Spine #184)
The Stars Are Beautiful (Brakhage, 1974) (Spine #184)
Stellar (Brakhage, 1993) (Spine #184)
Study in color and Black and White (Brakhage, 1993) (Spine #184)
Wedlock House: An Intercourse (Brakhage, 1959) (Spine #184)
Window Water Baby Moving (Brakhage, 1962) (Spine #184)
The Wold Shadow (Brakhage, 1972) (Spine #184)

nice work GuamGuy

yeah much thanks...