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I won't divulge my personal preference here, but here are the facts:

Common:
Same points cost
Poison

Blowpipe (threat range 18", but see Cons, below):
Pro: Multiple Shots
More Range
Con: If moved+long range+multiple shots, they do NOT count as poisoned (need 7's to hit)
Almost never hitting on 4+, as you will be firing multiple shots at least, and probably either long range or moved as well)

Javelin+Shield (threat range 14")
Pro: Always hits on 4+ (doesn't count moving, doesn't count long range)
Have 6+ Armour save
Have 5+ Armour save in Close Combat (hand weapon and shield)
Con: Lower range

What are people's thoughts?

Viperion

I would always take the blowpipes. The longer range is great for sitting in cover and annoying the gak out of your opponent. Javs don't have enough range for your opponent to not easily avoid them. I think the extra armor save is a moot point because I won't try and rely on skinks in CC no matter what. Just my two cents.

the blow pipes are better because once they are in the wood they can happily threaten giants etc with their poison trust me, i have an all skink list had they kill ogres,minotaurs anything big quite quickly

Personally, i take blowpipes due to the longer range. Sure the javelins hit more often, but you have to be REALLY close to a unit which can make it difficult to evade the unit's charge.
Really, I wouldn't care if skinks got a 3+ armor save in close combat. They're still toughness 2, which means they'll never make it far against anything besides fodder units while in CC.
Also, in the situation outlined above where they would only hit on 7's, I'd just opt to only fire once so I still hit on 6's. Statistically, you'd still have the same number of hits, only going with fewer shots you don't have to roll to wound. I remember seeing someone do the math-fu on this and it turned out that against most enemies, javelins only proved better at 6"-8" away from an enemy unit, where blowpipes take the additional long range penalty, but javelins are still within range.

blowpipes have done more for me in more battles but i have found that a mixture of the two in separate units works nicely. those units that will be more open to or look like they will be charged more i give javalins. any units that i will use at range or will advance more slowly i give blowpipes.