What determines the amount of condition damage from conditions applied by sigils and traits

Both of the links you provide say "Stacks in duration". According to the Effect Stacking page

Effects stack in one of two ways: in intensity or in duration. For example, multiple stacks of bleeding, which stacks in intensity, increase the damage dealt over time, and multiple stacks of regeneration, which stacks in duration, increase the duration that the healing over time lasts.

It also says

The best intensity lasts for the cumulative duration

Originally I interpreted this to say higher damage trumps lesser damage but increases duration which is incorrect. Based on info I found at Guild Wars Insider the answer becomes a little more complicated.

Multiple duration effects are applied in sequence for their applicable lengths of time. In this example lets say Chilled got applied then Crippled within 10 seconds of each other and both effects are for 60 seconds in length. Chilled would get applied to you for 66% reduction, Crippled would wait until Chilled had finished then immediately get applied to you for the 50% reduction for another 60 seconds.

The blog post at Guild Wars Insider has a nice graphic to show how this stacking occurs if my explanation is confusing.

So it turns out this is very easy to test on a Rifle Warrior, since their auto-attack causes a single bleed, and the default warrior loadout includes a bleed increase.

In short, conditions only deal damage for full seconds. 7 and 3/4 seconds will still only cause 7 ticks; you need that last 1/4 if you want 8 ticks.

So for bleeds, at least, you want to make sure that you're not wasting traits or runes on half-ticks or quarter-ticks. Either up your bonus duration, or find something else.

For Fire and Poison, it's a little different, because reapplying the condition extends the duration. In this case, the duration bonuses are a little better with fractional ticks... as long as you can routinely apply the condition. 5 1/2 sec burn + another 5 1/2 sec burn will give you 11 ticks, which means your bonus duration is not wasted, you just have to put in more effort to get a return on your investment, as it were.