Right, as lack of answer, I'll give a brief overview of my favourite mods:
Medieval Total War:
The XL mod rules, adding factions, enhancing the map, and generally being better than the original game. Search the mod subforum of the game here at the Org and you should find a download link.
Rome Total War:
Europa Barbarorum: Starts in 272 BC, adds factions, is the most realistic mod yet, I believe. Look in their mod subforum to see what it's like. And, if you have questions, ask the team. They're very helpful.
The First Triumvirate: Play as Caesar, Crassus, Pompey before, or during the Civil War. Play as the Gauls trying to reconquer their homeland from Caesar, or play as Parthia trying to stop Crassus' conquests. Very nice, and really good time playing it. Check Total War Center to download.
Rome Total Realism: I liked a lot for a time, but that was before I really played EB. Those two mods are more or less adversaries. Try them both. Check their forums, or check Total War Center for it.
Roma Surrectum: Changes the factions, makes the game better. Nice mod. Check the subforum here.
Terrae Expugnandae: the first RTW mod I played, done by Lusted, a pillar of the modding community, I feel. I played it for over four months. Look over at Total War Center to download it.
SPQR: Concentrates on the battle part of the game, but still gives in nice features for the campaign map (triumphs, rebellion). Check out TW center for it.
Barbarian Invasion (some mods are restricted to BI, that is, they use features from BI that are not compatible with RTW)
Invasio Barbarorum: Mod in the late Roman Empire (after the seperation between East and West) that offers one heck of an experience. Play as any Roman faction and your in for some great time. Check their subforum here.
Chivalry Total War: A mod set in the early period of medieval times. It's pretty nice, and the timeline chosen is pretty rare for a RTW mod.
Fourth Age Total War: If you're a Tolkien Fan, play this.
M2TW (Note: I haven't actually played any of them)
Lands To Conquer: Ever since I played Terrae Expugnandae, I was on the lookout for more of Lusted's work. He did this. When I get M2, I'll download this. You can find it here.
Medieval 2 Total War mods for now are in what I feel is an early stage. Medieval Total Realism hasn't been released yet, and Europa Barbarorum II hasn't been much talked about yet (at least, we know it will come someday). But, if you check these forums, you should find enough material to spend a good time.
Of course, these are only my favorite mods. This is because I like the Roman Era a lot, like realism, like Tolkien, etc. But you may have different interests, and may like different things. Therefore, I encourage you to try any mod that looks interesting to you. If you don't like it, just uninstall it, and find another.
It's your choice.
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