Importing referenced geometry, leave as imported body or run FeatureWorks

Are you talking about Import Diagnostics or FeatureWorks? 

All Import Diagnostics does is verify that the solid body information is valid.  That will make sure that mass properties, appearances, etc. will work properly with the imported body.  I have never seen Import Diagnostics actually increase the number of features in the tree unless the import is just so horrible that it creates a whole bunch of imported surfaces. However, in that case you wouldn't get a single solid body.

There is no need to run FeatureWorks unless you want to edit the feature definitions of the part.  Usually, even if you want to modify a purchased part you can still just add to or cut from the original imported body.

I'll not change the part into features unless I need to.

Chris,

I prefer to leave imported items alone.  With the exception of fixing import errors using import diagnostics (the flag irritates me to no end that it propagnates up to the next assembly).  Also changing color (paint by numbers) to make the part look more realistic...

Oh, and one other item... If I don't like the origin or want it to be different for PCB design I will fix that.  (Insert Ref. Origin, roundtrip step, etc)

Example...

if they are store bought parts and you are not modifing them, then no I would not spend\waist time in making it into features.

JMO.