[Powder]

-Sachs as Shredder
-Baxter Stockman's involvement
-Kevin Eastman's cameo (as a lab assistant)
-Foot Clan "super soldier" experiment plot & scenes (which included Vern & April stumbling upon the room where they're being mutated)
-Foot Clan member committing Hara-Kiri before The Shredder
-Numerous fight scenes
-April & Raph's trench coat excursion through Times Square
-April & Karai's fight scene
-Vern being in the lair with April & the turtles
-Michelangelo's guided tour of the lair

At least this much.

There was also talk of the Foot Clan being militarized so that the scene where they have a war in the streets with NYPD (& possibly the army, too, iirc) would be on more level playing ground, but I don't know if this was cut from the script or if they actually filmed parts of it & took it out.