Many series have had Thanksgiving episodes, which I do not consider "specials." Still, I suppose I might as well at least list some of them, in passing. At least the ones I personally remember (even vaguely) seeing; surely there have been many I've seen that I've forgotten, and many more that I've never seen at all. I'm not going to be saying much of anything about the episodes here, so perhaps you'll find the links useful.

Gilmore Girls
Season 3: A Deep-Fried Korean Thanksgiving (Amazon; A.V. Club; IMDb; Wikia)
Season 6: He's Slippin' 'em Bread... Dig? (Amazon; IMDb; Wikia)

Glee
Season 4: Thanksgiving (Amazon; A.V. Club; IMDb; Wikia; Wikipedia)

Heroes
Season 4: Thanksgiving (Amazon; A.V. Club; IMDb; ; Wikipedia)

How I Met Your Mother
Season 1: Belly Full of Turkey (Amazon; IMDb; TV Tropes; Wikia; Wikipedia)
Season 3: Slapsgiving (Amazon; A.V. Club; IMDb; TV Tropes; Wikia; Wikipedia)
Season 5: Slapsgiving 2: Revenge of the Slap (Amazon; A.V. Club; IMDb; TV Tropes; Wikia; Wikipedia)
Season 6: Blitzgiving (Amazon; A.V. Club; IMDb; TV Tropes; Wikia; Wikipedia)
Season 7: The Rebound Girl (Amazon; A.V. Club; IMDb; TV Tropes; Wikia; Wikipedia)

Life Unexpected
Season 2: Thanks Ungiven (Amazon; IMDb; Wikia)

The Michael J. Fox Show
Season 1: Thanksgiving (Amazon; A.V. Club; IMDb)

The Middle
Season 4: Thanksgiving IV (Amazon; A.V. Club; IMDb; Wikia) There's a Thanksgiving ep every season, but I think this is the only one I've seen.

Modern Family
Season 3: Punkin Chunkin (Amazon; A.V. Club; IMDb; Wikia; Wikipedia)
Season 6: Three Turkeys (Amazon; A.V. Club; IMDb; Wikia; Wikipedia)
Season 8: Thanksgiving Jamboree (Amazon; A.V. Club; IMDb; Wikia; Wikipedia)
Season 9: Winner Winner Turkey Dinner (Amazon; A.V. Club; IMDb; Wikia)
Season 11: The Last Thanksgiving (Amazon; A.V. Club; IMDb; Wikia)

Murphy Brown
Season 4: Mission Control (IMDb; Wikia)
Season 11: Thanksgiving and Taking (Amazon; IMDb; Wikia)

The Neighbors
Season 1: Thanksgiving Is for the Bird-Kersees (Amazon; IMDb; Wikia)
Season 2: Thanksgiving is No Schmuck Bait (Amazon; IMDb; Wikia)

New Girl
Season 1: Thanksgiving (Amazon; A.V. Club; IMDb; Wikia)
Season 2: Parents (Amazon; A.V. Club; IMDb; Wikia)
Season 3: Thanksgiving III (Amazon; A.V. Club; IMDb; Wikia)
Season 4: Thanksgiving IV (Amazon; A.V. Club; IMDb; Wikia)
Season 6: Last Thanksgiving (Amazon; A.V. Club; IMDb; Wikia)

Northern Exposure
Season 4: Thanksgiving (IMDb; Wikia)

The O.C.
Season 1: The Homecoming (Amazon; IMDb; Wikia)
Season 4: The Cold Turkey (Amazon; IMDb; Wikia)

Parenthood
Season 2: Happy Thanksgiving (Amazon; A.V. Club; IMDb; NBC)

Picket Fences
Season 1: Thanksgiving (Amazon; IMDb)

The Real O'Neals
Season 2: The Real Tradition (Amazon; IMDb; Wikia)

Scream Queens
Season 1: Thanksgiving (Amazon; A.V. Club; IMDb; Wikia; Wikipedia)

The Simpsons
Season 2: Bart vs. Thanksgiving (Amazon; A.V. Club; IMDb; OHS Wiki; TV Tropes; Wikia; Wikipedia)

Single Parents
Season 2: Every Thursday Should Be Like This (Amazon; IMDb; Wikia)

Smallville
Season 10: Ambush (Amazon; IMDb; Wikia)

Son of Zorn
Season 1: The Battle of Thanksgiving (Amazon; A.V. Club; IMDb)

South Park (There are other Thanksgiving eps, but these are what I remember.)
1997 short: Jay Leno Thanksgiving Special (Wikia; YouTube)
Season 15: A History Channel Thanksgiving (Amazon; A.V. Club; Hulu; IMDb; Wikia; Wikipedia)

The Spectacular Spider-Man
Season 1: Nature vs. Nurture (Amazon; IMDb; MAU Wiki; TV Tropes)

Speechless
Season 1: T-h-a-- Thanksgiving (Amazon; IMDb; Wikia)
Season 2: B-r-i-- British I-n-v-- Invasion (Amazon; IMDb; Wikia)
Season 3: C-e-- Celebrity S-u-- Suite (Amazon; IMDb; Wikia)

Sports Night
Season 1: Thespis (Amazon; A.V. Club; IMDb; TV Tropes; Wikia)

Stumptown
Season 1: November Surprise (Amazon; IMDb; Wikia)

Suburgatory
Season 1: Thanksgiving (Amazon; A.V. Club; IMDb; Wikia)
Season 2: The Wishbone (Amazon; A.V. Club; IMDb; Wikia)

Sunnyside
Season 1: Too Many Lumpies (Amazon; IMDb; Wikia)

Supergirl
Season 1: Livewire (Amazon; A.V. Club; IMDb; TV Tropes; Wikia; Wikipedia)

The Unicorn
Season 1: Turkeys and Traditions (CBS; IMDb; Wikia)

WKRP in Cincinnati
Season 1: Turkeys Away (Amazon; IMDb)