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You cover a good deal of the usual suspects, and, while sugar (et al) has been mentioned and its/their dangers more widely known, refined grains (which is really the only way that grains can be consumed) and grain products (like breads, chips, crackers, cereals, etc...) have pretty much gotten a free pass. That stuff, in all its forms (especially "healthy" whole wheat), jacks the wild blue heck out of your insulin. Namely:
Two slices of whole wheat bread have a higher glycemic index than 2 tablespoons of table sugar - meaning, it sends your blood-sugar skyrocketing. The massive amount of refined carbohydrates in wheat readily convert to glucose (the more refined, the quicker to convert), which triggers an over-abundance of insulin release (taxing the hell out of your pancreas in the process), pushing that glucose into your cells to be stored as fat (since nothing short of an Olympic athlete training regimen can burn it off as energy first). And, it goes far beyond visceral fat, affecting every organ/system in your body.
The gluten protein in grains contains a whole host of other problems:
Gluten: What You Don't Know Might Kill You
Wheat itself was only introduced in the human diet 10,000 years ago (less than a drop in the bucket of our evolutionary biology...so our system is ill-adjusted to process it, if at all), and scarcely resembles the overtly crossbreed/hybridized "dwarf" wheat that we consume today (along with all of its additives and "enrichments"
. Its "early ancestor," Einkorn wheat, was much more "simple" (containing only 14 chromosomes as opposed to modern wheat's 42...which, among other things, has severely altered the gluten structure, which has led to the type of gluten intolerance you see today), and could only be consumed as a porridge. Since its time, it has been crossbreed and hybridized (especially in the last 50 years) to the freakishly short "dwarf" wheat (variants of Triticum aestivum), which is high yield and low-cost at the complete expense of human health (it never underwent any trials to test its safety for human, or animal, health). In short, it's genetically frakked, which messes with our genetics when we consume it. And that wheat is upwards of 90% of the type used in all breads/pastas/boxed meals/chips/cereals/crackers/etc...
This book is great for a comprehensive rundown, and details some pretty startling health turnarounds when wheat was completely eliminated from one's diet:
Wheat Belly: Lose the Wheat, Lose the Weight, and Find Your Path Back to Health
And, to your point, it most certainly effects mental health. Everyone has turned the phrase 'you are what you eat' into a giant joke, but it is the truth. Our bodies are food recycling machines. And, whether or not people would like to admit it, or accept, what you eat is the raw material of every cell of your body - that includes your brain.
Among other resources (like the aforementioned book), there's a great documentary on it here:
Feed Your Head
Here's another thing that actually ties back in with the OP - that eating wheat (with its constituent metabolic effects) actually INCREASES APPETITE. And if you are constantly hungry, you'll eat more, so you'll by default consume more calories.
The health turnarounds when eliminating wheat from one's diet (see the book, or some of the reviews at the above link) are nothing short of amazing. In addition to shedding visceral fat, people have eliminated their allergies, joint pain, "bad" cholesterol ratios, mental fatigue, stress, low energy, constant hunger, rosacea, and an incredible host of others (including many chronic ailments).
Another great book to check out (which is broader in scope) is:
Deep Nutrition: Why Your Genes Need Traditional Food
I've focused mainly on grains/wheat here, but it absolutely includes everything else you mentioned. That's not to mention an almost more depressing fact, that even when we eat a good deal of the fruits and vegetables from supermarkets, we are getting more (or less, when it comes to nutrients) than we bargained for...
Tomatoland: How Modern Industrial Agriculture Destroyed Our Most Alluring Fruit
that researchers are overly-eager to study us all to the nth degree 
and the increased longevity, leads to more "exposure" to all the diseases that are age-related
