As usual, a big part the system to use/ depends on the tone, genre, and intent of the game. HP works great for me in D&D (which I consider it's own genre), but something much harsher would be warranted for something like a Twilight 2000 game. Though I don't think I would ever go to the level of (false) precision of something like Phoenix Command and it's 63ish hit locations...
For many of my high-adventure type games, I've really been liking the balance of Cortex Prime's Stress mod with a single Stress track. As the character suffers violence, fatigue, mental hardship, psychic blasts, and etc, they accumulate Stress (tracked by a die rating between d4/d6 up to a d12). As this Stress die can be added to an opposition pool, it has immediate impact (though note that the way the dice system works, while a high Stress die is noticeable and significant, it also isn't so harsh that it guarantees PC failure). If Stress is pushed beyond d12, then the PC is Taken Out (they are out of the scene) and they gain a d6 Trauma die based on what took them out. Next scene, the Stress is removed but the Trauma die remains, and as with Stress that Trauma die can be added to the opposition pool. And while Stress typically will automatically step down some amount after each scene or downtime, Trauma requires active treatment and is therefore more lasting. Additional Trauma gained of the same type steps up the Trauma die, and if a Trauma die goes over d12, the PC is beyond help and is out of the campaign (dead, mentally broken, etc).
For our group this is a nice sweet spot that provides for a meaningful downside of incurring hardship (vs the 100%/0% binary of something like Hit Points) without becoming too harsh of a death spiral, both because Stress recovers easily but also because being pushed over Stress only removes the PC from the scene and doesn't "kill" the character. It's also easy to resolve and to keep track of.
Cortex also has open-ended and situational consequences that can be applied for things that aren't as all-encompassing as Stress. (And when they apply, they are mechanically handled in the same manner as Stress.)
Putting aside Cortex's specific way of doing it, that's the kind of system I find works best for many of our campaign types. Legend in the Mist (with its Tags and Tracks), FitD (with its Stress/Harm/Trauma -- bit harsher but it often fits the tone), FATE (with its Stress/Consequences), these all fit in the same mold. For my Star Wars game (which is using my own system) I've currently got it set as a series of Stress tracks with specific Condition levels (and much like Stress/Trauma, Stress recovers easily but the Conditions require active care).