I whant to start this tread to see how others handle their workflow, what type of software mismatch you work with and all the weird combos.

For my self I run most of my files trough a Kodak Prinergy Powerpak workflow for normalizer, I rely heavily on Pitstop to make modifications, ill use mostly Pandora for imposition but sometime ill use Preps Ganging, ill proof all this with GMG DotProof running a Epson 9800.
And as far as the rest goes, Here's a small list of my favorites.

Scoop For CS3 ( illu plugin )
Genuine Fractals
PDF merge
Hot Door Cadtools
Concatenate ( illu plugin )
PDF Multipage Import ( Indd script )
FontAgent Pro 4
XMPIE ( Indd plugin )

and many more.

Please share your list so we can find out more ways to treat our files ...