Mysteries & Alignment
When writing a mystery storyline for my games I consider alignment a huge factor. One, what is the alignment of the villian. Probably LE (chaotic is tautologically too chaotic), though NE works as well. Far more important, however, are you PCs' alignments. If the majority of the PCs are pretty standard CG, then feel free to make your "villian" CG as well, or LG. This makes for a much more engrossing story because even the most righteous paladin is tempted to evil at times, he has that within him.
As an example (using a simple murder mystery), the victim is a local merchant & philanthropist, skewered at sword point in an alley on a rainy night. If this is how your PCs first hear of it, they're probably not in full-on pick every detail apart mystery mode yet. They'll probably assume it was thieves. Add the detail a bit later that his pouch was taken & you'll have cinched it for them.
But if through your carefully crafted discovery process they learn that the "villian" is actually a local hero (even a paladin) who was being black-mailed by the "philanthropist." Now, they've solved the mystery and they're probably still confused. "Was that justified?" "What do we do?" Now, you've forced them to consider their own characters & alignments and what's right & wrong. This can be even more fun. In all likelihood, they'll try to go subdue the paladin, but how do they go about it. What if the town reveres him, and don't believe the PCs. What if they secretly all detest the righteous little hero, and would lynch him at the first sign of wrong-doing but the PCs know that, despite a few bad acts, he's a good guy and has done a lot for the town. This kind of stuff can really add a bunch to your adventure and make it more memorable, IMO.
Z