Bob's and Angel's mods are my favorites. I like to plan more complex systems with waste products. I appreciate also that these mods are somewhat based on real world so that recipes are easy to understand and remember if I have basic knowledge about chemical processes in industry. Some other complex mods with fully fictive materials and recipes are very hard to get really into.
Other than the bottom two (and RSO); none of these mods adds or modifies entities. I tend to use all of these in practically every save (and I'm kinda leaning towards using Picker Extended on some saves.)