My most used abilities have to be:
Concussive shotArcane ShotSerpent StingRaptor Strike
Abilities that I love to use, but are specialized:
Rapid ShotMongoose BiteWing Clip
Least used abilities, due to ineffectiveness:
Scorpid StingDistracting ShotDisengageMulti-Shot
I play my hunter very differently than I imagine most people do. I'm the kind of hunter that would have really liked to have been a warrior, but loves shooting and having a trusty friend around. With that said, I often like to get my hands dirty in toe-to-toe fighting whenever I can (usually against mobs my level or below--Hunters are just about useless in melee against high-yellow or orange fights), so naturally I use Raptor Strike as often as I can to get that DPS up. Being in melee also allows me to use Mongoose Bite as long as I have agro (which usually only happens against green mobs, as Pete the Bear can't keep up with my damage against the weaker mobs). Mongoose bite is an ability that makes you really want to be in melee, because it makes the player be more involved in the combat and not simply a spectator. The same can be said for Wing Clip, as you can't use Concussive Shot when you're hashing it out up close.
As I do like to engage with more than my rifle, I know that Hunters are marksmen and that their power lies in their skill with ranged weapons. That in and of itself explains why Arcane Shot is on my list as most used, it's added damage that's there simply to add damage; it's free DPS. I will use Arcane Shot as soon as it's ready unless I'm on the verge of yanking agro away from my pet. Serpent Sting is nearly the same, added damage at a fairly reasonable MP cost. I was conflicted at one point, thinking that Scorpid Sting would be much more effective and that it would trump my need for poison damage. Even after buying Scorpid Sting: rank 2, I rarely use it. It's nearly worthless unless you're fighting extremely tough mobs with massive HP, it doesn't help your Pet out much, and you kill normal mobs that much slower. Serpent Sting's trickling damage is far more useful IMO.
Concussive Shot is phenominal and I use it fairly regularly, but not 100% of the time. I usually open up with Serpent Sting when my pet is close to the mob--to get it's attention to control how far my Pet has to go and to make sure he doesn't pick up any adds that I didn't see. I do use Concussive Shot heavily on "chicken mobs" when they get into the red, so my Pet and I can finish the job when they tuck their tail and start making it for their buddies. Stunning, or simply slowing, running mobs has saved me from innumberable adds and kept Pete the Bear alive in countless situations (damn impetuous bears!).
Rounding out my list were two anti-agro abilities, which either I simply don't know the power of, or they don't jive with my play style. Disengage I have never used, I never seem to get pull duty in groups and I rarely get agro in fights that I have to pull out of to fall back to a shooting position. Distracting Shot, beyond simply not being able to get enough agro to pull away from a Growl4 Bear, isn't something that I find I need to use much and is listed as such. Speaking of not using a skill much, Rapid Fire is one of those skills that I just love, but can't use regularly. It's great in "OH ****!" moments, when you absolutely must put the smack down or die, but otherwise you run too much risk of yanking agro off your pet.
Multi-Shot is useless right out of the bag, unless you're in a group and all Hell has broken loose (AND you're confident you wont pull two adds onto your ***, healers HATE having to watch over too many health bars) and you can afford to plink some damage into a couple more targets. Even in that case it doesn't cycle fast enough to really be of much use. You might use it against weaker mobs that you feel confident about tanking along side your pet, but that situation disappears quickly as your level raises.
All in all, there is a place for most of the abilities that Hunters have. All of the Aspects are usefull, though AoM is a bit underpowered as you level, but Hawk and Cheetah are invaluable in their respective rolls. Really what it all comes down to is how you want to play your Hunter: I may not feel the need to use some abilities, but someone else might use them to spectacular effect. It's all in how you want to play the game.
Good luck!