I think mine's probably Tauric. I guess I just like the idea of combining two creatures into one without using one of too many 'Half-templates.' I've used a lot though, but that's my all-time favorite.
I'm a big fan of the Amalgam template from Advanced Bestiary, in the vein of the tauric template. Want a wierd dinosaur cultist? Bam! Stegogresaurs, ready to go! A leader for an ape tribe corrupted by the Far Realm? Bam! Girillithid! So many options...
Stonebones Curse (Shaping the Self)- leveled templates have their uses and being turned into a gargoyle is a fitting punishment inflicted by some gods
Non-Euclidian (BOT DE)- for all my Cthulhu-y needs
Monsterous Lycanthrope (AB)- weretreant ogres are just too cool
Insect Scion (B&S)- the ultimate insect template
Half-humanoid (BOT DE)- so much one can do mad scientist style
Spirit (BOT DE)- I like the idea of disease and other monsterous spirits
Crowd (Minions)- The ooze that can be used for so much more than a monster
Jotunblood Giant (AB)- makes giants more giant
Savant (AB)- I need brainy creatures
Skoth (TT1)- the template for those who like to customize skum
Waterscale (and similar) (TT2)- I like nagas
Others include the child of light/child of darkness and ghoul/ghast from PFB and messenger from Brixbrix's Creatures of Ados.
Like the insect scion in Bodies and Souls, this is a template with a lot of options. Unlike that one, this is also limited since it is based on a Zerg like creature. But that can always be changed, of course.