Pathfinder is pretty clear about the ability to stack templates, as there are multiple published examples of such. At issue is that some templates would seem mutually exclusive if templates are applied consecutively; for example, both Skeleton and Skeletal Champion are "an acquired template that can be added to any corporeal creature (other than an undead) that has a skeletal system".
Would it be possible for a spell caster (or pair of spell casters) to impart both the Bloody variant or Burning variant Skeleton template and the Skeletal Champion template onto the same corpse to yield a Bloody Skeletal Champion? Mechanically, if allowed, simultaneity of animate dead and create undead (the spells used in creating these templates) could be achieved by readied actions or contingency spells — so that's not an issue. The issue is entirely that consecutive application would yield a creature of a type invalid for the second template.
Best Answer
In 3.5, Templates are always applied consecutively:
(from Improving Monsters)
Pathfinder, however, occludes the templating section in its advice on monster improvement. This means that, while the developers presumably still intend templates to be applied one-at-a-time, no rule indicating that actually exists in Pathfinder. Thusly, the answer is not specified by the rules, as written.
Since simultaneous application is not possible in the general case, however1, not disallowing simultaneous templating will lead to seriously problematic undefined behavior (though not during game sessions).