The answer is there is no preferred one. Everyone does something a little differently. There are generally preferred cast sequences, but how they are implemented in a multibox setting is completely different for everyone. Mostly due to procs or spells that require mouse intervention. Also, keep in mind the optimum cast sequence often differs between bosses and trash [and possibly more if you raid or just do heroics].

What I use

My Boomkin:

macro 1 /castsequence Faerie Fire (bunch of commas)
macro 2 /castsequence Insect Swarm (bunch of commas)
macro 3 /use 13
/use 14
/castsequence Moonfire(bunch of commas)
macro 4 /castrandom Wrath, Wrath, Wrath, Starfire, Starfire

I have a single button that clicks all four of these in sequence such that the Faerie Fire, Insect Swarm and Moonfire are only applied after they are about to fade (using commas).

I take the loss on Eclipse procs, which is something I will work toward changing. I have been playing around with the Powerauras and Miks SCT addons to do this (for my mage procs too).

My Shaman:

Macro 1 /cast Elemental Mastery
/use 13
/use 14
/castsequence Flame Shock( bunch of commas)
Macro 2 /castsequence Lava Burst (bunch of commas)
Macro 3 /castrandom Lightning Bolt, Lightning Bolt (don't really need to do this, but I had chain lightning there but took it out)

Again, I have a macro that clicks all three of those macros and the timing (using commas) is such that Flame Shock and Lava Burst are cast at the approximate appropriate times.

These are not my exact macros, but you get the basic idea of what I am doing. I based my macros on cast sequecne information I obtained from the Elitist Jerks website. It can be difficult to implement the ideal cast sequence without heavy micromanagement due to procs etc.

Anyway, this is the way I do it. It is probably not the best and there are most likely much better ways to do it. I haven't really tested these against other more simple macros or straight spell spam (e.g., like Wrath or Lightning Bolt spam only) to see which provides the best DPS. My current DPS seems to work for ok for me for what I do. Some day I will spend the time to test it all out. It took me several hours to work out my Mage DPS macro and I am still not happy with it. So, some day!!

Info on Spell Rotations

Elemental Shaman spell rotation taken from here .

Rotations
  • Fixed Rotations
    The fixed rotation is based on a set number of spells in a set order. An example of this would be the 8/1 Fireball/Scorch rotation of Fire mages (or Frostfire/Scorch for the Frostfire builds). Generally the rotation will be FS, LvB, CL/LB filler, LvB, CL/LB filler, and repeat. CL can be used 2-4 times in this rotation, depending on cooldown management. CL is useful here in that it can help reduce that "filler" time to allow the next LvB to be cast sooner. Also, with a fixed rotation you are likely to clip 1-2 ticks of the Flame Shock dot.
    • Waiting for Cooldowns
      There are two methods of handling the cooldowns in a fixed rotation. The first (No-Wait) is to simply ignore the fact that cooldowns may be coming up soon, and use the best spell available. The advantage is that there is no wasted time, but you may be pushing the next LvB use out past the 8 second cooldown, reducing DPS. Whereas the second method involves waiting for the next cooldown (be it CL or LvB). The downside of waiting for cooldowns is that it is a fine line between wasting too much time, and letting cooldowns go unused. Ideally, the best solution is to swap between the two based on your own judgement.
  • Priority Rotation
    In a priority rotation, there is no set cast order (this is a concept that has been used by Shadow Priests for some time now). All you do is use the highest priority spell that is available. Generally, this will be FS>LvB>CL>LB, although it should be noted that Flame Shock should be recast, and clip the last tick, if Lava Burst will be off cooldown and the cast finishes after the DoT expires.
  • Earth Shock
    There are some people suggesting that Earth Shock be used in rotations as well, with the ES glyph that reduces the GCD when it is used by 1 second. Currently however, this is not functioning correctly, and reduces the GCD to 1 second instead. Even with this fixed, it is still somewhat dubious as to how much of a gain it will be, especially with the 25 yard range (with talents).
  • Chain Lightning
    CL can be used in single target rotations, as it has a slightly higher DPSC (or Damage Per Second Casting) figure than LB. The trade off is that the mana cost is much higher (and disproportiantly so compared to the dps gain). There is also suggestion that using it in place of LB just before the LvB cooldown is up can increase dps as well, and while this is a good point, you would either have to be running a fixed rotation, or be able to discern which spell to use at which point. Generally, I would recommend using a CL in every LvB cooldown that you don't cast FS in, for either fixed or priority rotations, if you want to do this

Boomkin spell rotation taken from here.


Spell Rotations

The Eclipse Rotation

You will generally operate in a three-step cycle.
1) Pre-eclipse. Cast Wrath until the Eclipse buff appears (have some mod that will make it very obvious when you gain the buff).
2) Eclipse. When you see the buff, finish casting your current Wrath and then cast Starfire for the duration of Eclipse. Note that a Starfire only gains the benefit if it is fully completed while the Eclipse buff is up, so if you only have time for a partial cast, your Eclipse is effectively over (and you'll typically refresh some DoTs here, see below).
3) Post-Eclipse. When Eclipse fades, cast Starfire for the duration of the Eclipse cooldown (you should have a mod to show you the duration of the cooldown). This is also the part of the cycle where you most prefer to cast any spells that are not Wrath or Starfire.

Roughly 1.5 seconds before the Eclipse cooldown ends, begin casting Wrath again. The goal is to have the Wraths start hitting the boss as soon as the cooldown ends, restarting the pre-Eclipse phase of the cycle.

DoTs

The basic principle with DoTs is that you want to maintain high uptime without cutting into your Eclipse time. As a general rule, refresh them anytime they drop and you're not in an Eclipse (there's currently some uncertainty as to whether you want to refresh them during the Eclipse). But once you've been running the cycle for a long time, some rhythms to DoT usage emerge, which I'll try to describe here.

Insect Swarm has a 14s duration, so you can cast it twice during the 15s Eclipse cooldown. Cast it the first time right as Eclipse ends (slightly before Eclipse ends, actually--as soon as there's no longer sufficient time for another Starfire during Eclipse). Cast it the second time immediately before starting your Wraths for the next cycle (this might sometimes clip a tick--try to get comfortable with the timing).

There are generally two ways to handle Moonfire.
1) Refresh it anytime it drops and Eclipse is down. This typically results in casting it once each cycle after Eclipse ends, because it will fall off during the next Eclipse and you will cast it again when that Eclipse ends. If you're unlucky proccing your next Eclipse, it will sometimes fall off during pre-Eclipse--refresh it and continue casting Wrath.
2) Refresh it once at the beginning of the post-Eclipse phase (right after casting your first Insect Swarm) and once at the end (right before casting the second Insect Swarm), clipping the first one. This results in near-100% uptime, at the cost of more frequent refreshing. This cycle is a bit trickier to manage well due to the clipping involved.
If using Glyph of Starfire, I'd recommend #1 (no clipping). If using Glyph of Starfall, both provide roughly equal DPS.

DoT refreshing always requires some improvisation, due to varying luck with Eclipse procs altering the length of your cycle, and interruptions or target switches at a particular encounter. The prior two paragraphs was a description of how things usually work out when you DPSing a single target for a long stretch with no interruptions. When in doubt, remember that your DoTs are high-damage spells and should generally be kept ticking on anything that's going to live for more than a few seconds.

Other spells

Starfall: use this on cooldown against a single target (if there are others mobs in range, remember to make sure it's safe to cast). The best time to use it is during the post-Eclipse phase, as this is when you benefit most from the added Nature's Grace uptime. In AoE situations, try to use it as often as possible on multiple targets.

Force of Nature: use this as many times as possible in a given fight. If you know when Bloodlust/Heroism is coming, try to cast this immediately beforehand (but not if this requires waiting so long that you can't use it as many times during the encounter). As you learn each fight, pay attention to things the kill the Treants and time your cast to avoid them if possible.

Faerie Fire: Unless your raid has both a Shadow Priest and a Feral Druid, keep this on every mob. Even if it does have both, it doesn't particularly hurt to cast this at the pull if you think there's a chance either of the other classes' buffs will ever drop.