Earth 2150's map editor allows vertical water to be created by some judicious placing and removal of capture-the-flag flags while terra-forming. The water is perfectly usable by in-game LC units, making it likely that it was meant to be included as a feature.
The data files for the Covert Operations expansion disc contained several music files that are not used ingame, including alternate versions of two already-existing songs that feature vocal samples, the songs used in the ending cinematics, and a few others.
The missions for the Unguided in Syndicate Wars might fit. They come from a third campaign that was dropped, but if you know how you can play them separately.
In the pre-release demo of Command & Conquer 3: Tiberium Wars, the player was supposed to only be able to play as GDI; the Scrin simply weren't in the demo at all, and Nod was to serve as an enemy only. However, they failed to disable some keyboard shortcuts as well as they meant to, and as a result enterprising members of the fan base were soon trying out the Brotherhood of Nod well before they were meant to.
Because most of the code was taken from the previous C&C game, Command & Conquer: Tiberian Sun, and simply rewritten, lots of TS names still exist in the code, for instance, technically, the code refers to the Allies as the GDI and the Soviets as Nod. Also, if you're curious, most of the TS superweapons are still in there, just dummied out and can be re-entered fairly simply, assuming you work around the ones that have been repurposed and you obtain the correctly sized animations for RA2's different resolution. This caused a now dead Game Mod called Command and Conquer Reloaded, which was RA 2 with everything from TS added in.
Which is why Final Alert 2, RA2's map editor, is apparently compatible with Tiberian Sun.
Red Alert 2 had three vehicles (A light tank, a mobile artillery and a transport helicopter) that were resonably complete, including artwork and statistics, but were not used in the game. The light tanks code was reused for Yuri's tank in the Expansion Pack.
Additionally, the Yuri's Revenge disc contains a few maps for what was probably going to be a single-player Yuri campaign. Among these maps is a large map of London, presumably the final level, loaded with triggers and sound files.
Command & Conquer: Tiberian Sun itself was littered with dummied out content... namely the Dropship Bay system, voxels for Tiberian Dawn and Red Alert 1-era units, and so on and so forth. In many cases, however, there are large portions of the assets still missing; there are no sidebar portraits for any of the TD and RA-era units, no art or rules code entries, and the units themselves are not designed to the same standards as the normal units (they are just flat colour/remap) and so on and so forth. There is also an unused flame tank from the first game. Famously, the beloved Mammoth Tanks from the previous games didn't appear except as non-useable units in a few scripted cutscenes. They were instead replaced with the "Mammotk MK II", a giant walker. It was, thankfully, very easy to edit the game file to restore the non-usable Mammoths in the build queue.
There were several units that didn't make the release build, but still had data files on the disc. This also meant that the two generals that heavilly relied on these units for their Generals Challenge maps, the Demolition (GLA) and Infantry (China) generals, had to have their maps cut from the random selection of the Generals Challenges.
In addition, there was initally going to be 3 bosses, one for each nationality. These, too, were cut but still have data files on the disc.
The Homeworld games recycled most of its rejected ship models to use as derelicts in 'starship graveyard' scenes, but a few items were only found with code digs:
The original game's code had a fairly complete version of a faster but more lightly-armed version of the Mighty Glacier of the game's various fighters, which was kind of redundant and left out of the release version, as well as textures for the lifeboat Narcissus from the first Alien film that was presumably intended as a Shout-Out/Easter Egg.
The sequel was originally intended to have support units, along with support frigates, drone carriers and something similar to the mobile cloaking field generator of the original game. Stats for ships associated with the latter two and some broken drone AI remain for the modding community to pick over.
A promotional demo disc of Homeworld was released under the title "Raider Retreat". It follows the first few missions of the game faithfully, which almost all deal with the Turanic Raiders, but the final mission in the demo is an assault on the Turanic Raiders' world, which doesn't appear anywhere in the game, and even had some special voice acting. A look at the game's data files reveals that it is present as "mission05_oem", but unplayable in the final version of the game. It was probably cut because it doesn't do much to advance the plot and also involves an excessive Difficulty Spike; the single Raider carrier you fight in Mission 4 was bad enough, but this level pits you against several of them! It can be watched in its entirety here.
Rock Raiders is just full of unused data, from giant web-making spiders to mobile teleports to sax-playing Raiders...
In Medieval II: Total War, you can make the Papal States playable by editing a single line in a game configuration file. This allows you to rampage across Europe with the Pope leading your dread army of Swiss Guards, lets you excommunicate other nations merely by declaring war on them and gives you full use of the Inquisitors as virtually unstoppable assassins. While playing the papal states Venice is capable of excommunicating you oddly enough.
There were also dummied out traits referring to heretic armies.
Looking up the data text files also shows the system the Papacy uses in the first Medieval exists, although no sound file exists.
In Rome: Total War there is residual code that suggests originally there would have been a second campaign called "Caesar in Gaul" presumably where you, as Julius Caesar, would have conquered Gaul, perhaps similar to the way the Viking Invasion additional campaign worked in the original Medieval: Total War. There isn't enough to start it up and no-one seems to have tried to create a Caesar in Gaul mod using it, though. The official expansions for RTW (Barbarian Invasion and Alexander) worked differently.
The First Shogun: Total War has files naming "Chosokabe". It can be more obvious that in one of the intro videos shows a Leader's Castle in The Tosa area. Many fans speculate that the Rebels icon in the select screen would've been for the Chosokabe clan, since the rebels, except the Alliance Chart, use different icons.
It also makes it obvious that in real life. The Chosokabe Clan was mostly in Tosa province during that time.
The files for Empire: Total War contain data for regions across the entire globe, but only Europe, the Middle East, North America and India made it into the final game.
Warcraft 3: In The Frozen Throne expansion, some spells and abilities that weren't used in the game can be found in the editor. For example, the Spell Breaker (and bandit creeps) have the animations to raise their shields to deflect magical/piercing attacks as the footman does, or Akama summoning felhounds instead of the standard spirit wolves. In addition, some units whose models were inexplicably changed (ballista to glaive thrower, catapult to Demolisher, Steam Tank to Siege Engine) can still be used, though it requires typing in the exact filepath.
These units were removed for legal reasons due to Games Workshop claiming they were too similar to units used in Warhammer Fantasy. They were retained on the game disc so that the original campaign could be played with the same disc as the expansion.