My thread choice is dependent on what kind of quilting I am doing and what look I am going for.
My go to thread for most projects is 40 wt trilobal polyester and my preferred brand is Glide but I have also used Isacord, and Metro and Sigma embroidery thread
http://www.metroemb.com/store/
I like the shiny look of trilobal poly. If I want a matte finish I will use 100% cotton. But some are so very linty they are at the absolute bottom of my go to list. Others, like Superior King Tut are quite nice and I have no issues with lint with King Tut.
For ditch work I like using a monofiliment like Superiors Monopoly or Filtec Essence. I understand YLI makes a wonderful monofiliment but I have yet to try it.
I have also done ditch work with Wonder-fil's thread Invisifil. Invisifil is a 100 Wt polyester and quilts like silk for a fraction of the price. It is awesome for doing ditch work and tight fills and in any application where I don't want the thread to show but want the texture. Another alternative to Invisifil is Decobob which is an 80 wt 2 ply poly.
I also love to use fancy and specialty threads like metallics both Superior and Wonderfil, holographic thread like Superior's Glitter. And I recently got some Wonderfil Spaghetti a 12 wt cotton you can run through the top! I can't wait for a project to try that one out in the longarm. I have already used it in a Sashiko project and it worked great. Have also used it to hand embroider labels.
I have used So Fine and Bottom line and they are both nice but I always seem to go back to Glide.
For bobbins I use magnaglides almost exclusively with very few exceptions. Both the Magnaglide delights which are loaded with Glide 40 wt and the magnaglide standard which are only available in a limited color selection and bulk. They are loaded with 60 wt glide.