Now that both of the original TV soundtracks, the FWWM soundtrack, and the Twin Peaks Archive have been released, here is a list of the (known) officially unreleased tracks:

Used unreleased tracks:
Completely unreleased:
Audrey's Walk (Earle's Flute) (Alternate Version)
Leland's Dance
The Swan (Instrumental)
On Bootleg:
Solo Percussion (Arbitrary Cymbals 2) [On Bootleg]
Sneaky Audrey (Reprise) [On Bootleg]
Released in altered form:
Americana (Original) [On Bootleg]
Stair Music (Danger Theme) (Full)
Freshly Squeezed (Fast Cool Jazz Clean) (Full)
I'm Hurt Bad (Original Studio Version)
Great Northern Piano Tune 4 (Clean)
You Killed Mike (Unmixed Full Original)

Used unreleased short tracks/sound effect tracks:
Completely unreleased:
Red Room Noise
Giant's Theme
Jacques Beats
Various Dark/Nerve Tones
On Bootleg:
Scary Sounds [On Bootleg]
Cooper Gets Shot [On Bootleg]
Saw Effect [On Bootleg]
Threat Tone [On Bootleg]

Unused unreleased bootleg tracks:
Dance Of The Dream Man (Flute & Synth Bridge)
Dance Of The Dream Man (Solo Vibraphone)
Freshly Squeezed (Slow Solo Vibraphone)
Laura Palmer's Theme (Ghost Version Alternate)
Laura Palmer's Theme (High Version)
Laura Palmer's Theme (Piano & Strings Bridge)
Laura Palmer's Theme (Piano A TK3 & Synth)
Laura Palmer's Theme (Harmonium & Synth Intro)
Laura Palmer's Theme (Harmonium Intro)
Laura Palmer's Theme (Solo Dark Synth)
Laura Palmer's Theme (Synth Passage)
Leo's Theme & Stair Music (Danger Theme) (Normal Speed) (Version 2)
The Mill Deal (Organ & Synth Reprise)
Sneaky Audrey (Organ)
Solo Percussion 5
Plotting Theme
One Armed Man's Theme (Clarinet & Bass Clarinet Combo)
Saw Effect/Suspense Music
Twin Peaks (Orchestral)
Twin Peaks (Bumper 1)
Twin Peaks (Bumper 2)
RR Tune 6
RR Tune 7
RR Tune 8
RR Tune 9
Ice-Rink Carnivale

Other known unused unreleased tracks:
Earle's Theme (Strings)
Dance Of The Dream Man (Original Solo Sax) [no echo]