DedIago: Third Age: Total War for Total War Medieval II: Kingdoms, great mod based on the Lord of the Rings story. Technically it's mostly the same Total War, but in Middle-Earth:
http://www.moddb.com/mods/third-age-total-war Also for M2TW: Kingdoms is Rage of Dark Gods mod (former Call of Warhammer). It's unfinished and corrupted by bugs, but fully playable. And anyway it's Warhammer FB!
http://www.moddb.com/mods/call-of-warhammer-total-war New Horizons mod for Pirates of the Caribbean changes gameplay, graphics, adds many new storylines take place in different times and places with different characters and unique gameplay features. Work in progress for many years, and every release adds something new:
http://www.moddb.com/mods/new-horizons Haha, I was about to post about the Rage of Dark Gods mod, good stuff:)
There is also A Song of Ice and Fire/Game of Thrones mod, Westeros:Total War
http://www.twcenter.net/forums/forumdisplay.php?721-Westeros-Total-War In a similar vein there are countless awesome TC mods for the Mount and Blade series, especially Warband.
A few of my favorites are:
A Clash of Kings, ASOIAF mod:
http://www.moddb.com/mods/a-clash-of-kings The Last Days of the Third Age, a LOTR mod originally for M&B, converted for Warband mostly by a guy going by Swyter
http://www.moddb.com/mods/the-last-days and
http://forums.taleworlds.com/index.php/topic,199243.0.html because you will probably need some help with installing the fixes, or just wait for the (hopefully) final patch.
Edit:I should mention that this is a true TC in that it actually gives you a Win-Loss scenario; either the Forces of Good (Dwarves, Elves, Men) or the Forces of Evil (Sauron and Co) will win the War of the Ring, and your actions for either side play a hugely significant role.
Warsword Conquest, a Warhammer Fantasy mod, now in beta stage and looking very good.
http://www.moddb.com/mods/warsword-conquest There are also countless mods for Neverwinter Nights 1 and 2, but I am not sure if any of them count as TCs since they don't change the mechanics, just the setting, characters, etc.
Happy gaming:)