I have not heard either the Martin Logon or the JL Audio subs, but based on testing and experiments with subs in my own room, I do have some comments.
Yes, Erik is right that room acoustics can play into subwoofer quality, but I think it will take a very large amount of bass traps to really take care of bass issues in the room.
That being said, if your priority is 60% for music, I might think the Martin Logan would be a better choice. The three opposing 8" woofers firing at the same time will help reduce cabinet resonance (although the top and bottom panels are still able to resonate somewhat). The triangle design helps as well. Having 3 woofers fire at different directions will probably help with room modes cancelling bass frequencies. The Martin Logan is probably going to have a more true sounding bass for music accuracy.
The JL Audio, on the other hand, is a single front-firing woofer with a beefier amplifier. This sub will hit harder on the bass frequencies with more SPL on your chest -- great for movie effects. The Martin Logan will probably be more accurate and you will be able to "hear" more of the bass tones, but you won't feel them. Any time you have a rear firing woofer, it reduces the amount you actually "feel". Also, you should make sure there's nothing on the wall nearby that can cause rattles/vibrations, as the rear firing woofer will definitely excite these elements more. The JL may be less resistant to cabinet resonance/vibrations.
I have heard an older Hsu subwoofer, 15" I think. When strong bass hit, I could hear the cabinet rattling like crazy - it definitely took away from the impact and effect of the bass if you hear half of it from cabinet resonance. (the sub was even vented, so it wasn't like a sealed cabinet with more internal pressure).
