It depends on what you want. Keep in mind that if you ask this here and in rAthena, you'll get here replies that say "Hercules is better" and in rAthena forums you'll be told that "rAthena is better". Correct reply is "Hercules is better in some ways, rAthena is better in some other ways".
We don't get any commission or whatever based on users, (unlike rAthena we don't even place adverts on our pages), but it's an administrator preference.
Here in Hercules we have the fastest and most optimized Ragnarok Online emulator to the moment and there's no possible argument to this: you can run the map server on 70 MB RAM, while rAthena consumes around 200 MB on an idle state. Anyways, this varies on the amount of maps and NPCs you load on your server, and in the amount of users you have. It's also a fact that Hercules consumes much less processing time than rAthena, but I'm not aware of how much. This also means Hercules boots faster than rAthena and has some caching system for even faster boot at the cost of some disk space. Note that these measures also vary depending on the OS you're using
Hercules has some features that rAthena doesn't, and vice versa. For example we have an anti WPE security system (depends on client version) and some unique features (some of them were also merged in rAthena). The same happens on rAthena side, but I'm not well informed on that.
Emulator stability is comparable, but since in Hercules we introduce and make more features it's quite obvious we are a bit riskier on that and may crash a bit more. Anyways, our bug fixing is way faster than rAthena. We're also comparable in emulator support, too, but I believe we've more answered topics in relation to our total amount that rAthena.
The biggest flaw I can see out there is on the scripting and db development side, since rAthena is more active than us on that side (in fact, we seriously lack on them). Anyways, you can generally import all of them here with very little to no effort, most cases it's just a copy and paste issue and they'll work. We're also lifting some IMPORTANT scripting limitations at the moment and have no information of rAthena doing that at the moment.
We've also support for the last 3rd job skills while rAthena doesn't (with good formulas but still not perfect), but neither of us have Rebellion yet.
And we've also have a plugin system that allow you to make new features without the need of creating conflicts in the source code when updating. Anyways I still don't know why third party devs like eAmod still don't want to support us because it's pretty damn easy to do that with the plugin system which was specifically designed for them. I prefer to think they're lazy bums and only want to sell, because in eAmod case they tell you they support Hercules but then when you buy it they tell you it's still in merging process (it's been like 3 months merging, seriously?). Anyways, it's not that I personally like that much people getting rich at the cost of our free emulator.
In short, if you want my opinion:
Performance: Hercules
Stability: If you mind it over all other things, use rAthena because it's slightly more stable but not much. Else it doesn't quite matter.
Support: Hercules for bug fixing, doesn't matter for forum support.
Development of new features: Hercules
Development of scripts: rAthena (but you can just copy them over here most of the cases).
Third party support: Still rAthena.