My favorite is Duke Patrick's. The hardest (overall), most realistic, and most comprehensive combat mod, it makes relatively huge changes to enemy combat behavior (no other mod is even close in this regard). It's heavily scripted, and always under development, so keep that in mind. Duke Patrick's mod is hybrid, both player skill/tactics and character skill are important. With Duke's you'll have groups of enemies try to surround you, and if they do, you'll end up dead. Wolves and other animals will power attack leap on you to knock you down. Bigger enemies strike you with more force, so they might knock you around. Higher level NPCs might charge into you to knock you down (and you can do this to them, too). There's a lot of cool behavior that I always miss if I use vanilla or other combat mods. NPCs also block a lot more, because unblocked strikes are very lethal. Momentum increases damage, and there are locational damage bonuses. It has a lot of other features, too. Depending on your mod setup and computer, you might have script lag. Also, because it's very actively developed, there may be short periods where a new feature is added that doesn't entirely work right. spookyfx, the author, has a very ambitious vision, so I think this is to be expected.
My runner-up is Combat Remastered. It takes a lot of what other mods (Deadly Combat, Duel, ACE, etc) have done, and respins its own version. It's got some good perk trees, too.
SkyRe and Requiem are complete overhauls (beyond combat), and what I consider RPG-style (more on that below). Others can comment in more detail, both of these mods are very popular.
Duel is another RPG-style combat overhaul. I haven't tried recent versions, so keep that in mind. What I mean by "RPG-style" is that they're very influenced by character skill, and downplay player-skill and tactics. So a low-level character will have very tough combat, while a high level character will have a lot of easy combat. I personally hate bashing an unarmored enemy in the face with a mace, and having them shrug it off because I'm not high-level (and a range of similar situations), so I'm biased against the RPG mods.
Deadly Combat is kind of a vanilla combat enhancer. IMO it does good changes to armor damage resistance, some enemy AI tweaks, a good stagger system, and makes blocking more important. It also amplifies both player and NPC damage to make combat faster and more deadly. IMO, this can be exploitable, encouraging you to charge in swinging. Recent versions have a very configurable MCM menu, though, so you can "fix" this if you think it's a problem. DC also has locational damage bonuses.
Ultimate Combat has some features similar to Deadly Combat (stagger, amplified damage), but doesn't make as many changes. It does add new enemy moves which are pretty cool, IIRC turning kill moves into normal attacks. It has an MCM menu for configuration. I thought it was fun to play, but is pretty much vanilla with a few enhancements. IIRC, it's occasionally buggy with animations getting stuck, but those are rare and not a deal-breaker unless you're super-sensitive about it.
ACE is good and very modular, and I used to use pieces of it together with Deadly Combat, but it's been so long since I used it that I can't say much about it. I do remember that it was frustrating to use it as a Battlemage, and IIRC it split bows into 2 types, which required multiple compatibility patches depending on your mods. I think Combat Remastered does this with bows as well.
Also, SkyTweak isn't a combat mod, but it has a few optional combat scripts and allows you to tweak a fair number of vanilla combat settings (among many others). If you want an improved vanilla system, this would be a good one to look at.