Here's an updated evaluation of the options for 3.3.3 glyph slots. The source for most of this is this post at EJ. Please note that the numbers posted a few weeks ago were using an early version of the 3.3.3 data and a fairly low gear level - this post reflects the (presumed) final state of 3.3.3 changes and accounts for higher gear levels too.
Top two glyphs
No contest here - Glyph of Lightning Bolt and Glyph of Totem of Wrath are our best two glyphs by a significant margin. Though they both give most benefit in stand-and-nuke Patchwerk-style fights, their value is not badly affected by high movement or "add"-style fights.
These two are a good choice no matter what, basically!
Third glyph
This is more up for grabs. The glyphs that are under discussion are as follows:
Glyph of Flametongue Weapon
This is strongest in stand-and-nuke fights, and both SimCraft and ZAP! have it slightly ahead for stand-'n-nuke at all tier 10 gear levels. It benefits all our spells except Lava Burst, though 2% crit is a comparatively weak bonus.
Glyph of Lava
This is really really close behind Glyph of Flametongue Weapon in the stand-n-nuke scenario. In the passes I ran with SimCraft it actually equalled Glyph of Flametongue at best-in-slot (277) gear levels. Although it only benefits one spell, that spell tends to be a solid part of our rotation no matter what the situation - and this its strength.
Glyph of Flame Shock
This is a fair bit behind at lower (251) gear levels, but by higher gear levels it's catching up again. SimCraft puts it slightly ahead in high movement fights at BiS gear levels (277) but this obviously depends upon early constant uptime with no "clipping". The advantage of this glyph is that, provided there is a target alive, Flame Shock will tick no matter what we are doing. The disadvantage is that Flame Shock contributes the least to our damage out of any spell in our rotation, so devoting a glyph slot to it is always going to be risky.
Glyph of Elemental Mastery
The important thing to understand about this glyph is that the 30 second cooldown reduction applies to the base cooldown of EM. With 4t10 and entry level haste, the effective cooldown reduction provided is only about 15 seconds. As haste gets higher and higher, the effective cooldown reduction gets lower and lower. (This is because the shorter EM's base cooldown, the less time we have to cast Lightning Bolts while it's cooling down.) Glyph of EM never becomes competitive with the other glyphs listed above.
Conclusions
Lava is basically the best glyph for burst, and probably the most "reliable" (i.e., least subject to variation) for any single target situation.
Flametongue is theoretically the best single-target stand-and-nuke glyph, as well as categorically the best for AoE.
Flame Shock is the outlier which might be worth consideration for advanced players at high gear levels. If you can Flame Shock multiple targets it gains value, but if those targets aren't surviving for long it loses value. For true AoE Flametongue still wins.
For me personally, the key thing about Lava is its reliability - it's about a thousand extra damage every time you cast Lava Burst which we wouldn't otherwise have (whereas FtW is just an extra 2% chance for damage we might have anyway), and Lava Burst is a key part of our damage in almost every situation. The only time Flametongue Weapon would move significantly ahead is for true AoE situations. However there's a definite competition between the two and a real choice to be made. Flame Shock should really be avoided unless you're really confident that you have a great reason to chance it.