These are the two most obvious ones, both their 1974 Pretzel Logic album.
"Rikki Don't Lose That Number" Listen close to the opening bass line.
The source of that bass line: The Horace Silver Quintet's 1965 recording of "Song For My Father" with Pittsburgh legend Roger Humphries on drums.
Their take on Duke Ellington's "East St. Louis Toodle-oo." Fagen himself plays alto sax, something he didn't do, to my knowledge, on any other Steely Dan recording.
Duke Ellington And His Washingtonians' popular 1927 recording of "East St. Louis" with solos by trumpeter Bubber Miley and trombonist "Tricky Sam" Nanton. Ellington had recorded an earlier version of the song in 1926, but this version is the first Ellington recording to qualify as any sort of hit. On Steely Dan's record, Walter Becker's guitar (with wah-wah effect) mimics Miley; Jeff Baxter's pedal steel emulates Nanton's trombone.
PS. On anohter topic, PG Pop Music Editor Scott Mervis wrote an exceptional story today on the Music Smiles organization bringing music to patients in local hospitals. Click here to read it.