I don't think, nutritionally, store bought honey is much different. It's not pasteurized or anything. Most honey at the store is filtered, but not all.
Honey is marginally better than sugar (and virtually all other healthy sounding sweeteners like "brown rice syrup," "evaporated cane juice," etc.).
Honey is sweeter than sugar, so you need less of it. Plus, it doesn't bump blood sugar as dramatically as sugar.
Here's a blurb and link...
Blurb
Diet & Lifestyle
Sugar Research
Honey sweeter than sugar
Simple carbohydrates in the diet, such as sugar are a recognized link between common degenerative diseases, such as dental problems, diabetes, heart disease and obesity.
A study was carried out to evaluate and compare fructose (fruit sugar), sucrose (sugar) with honey, to understand the different effects the carbohydrates had on glucose levels.
Thirty-three chiropractic volunteers were given a 75 –gm carbohydrate load in 250ml of water of either fructose, sucrose or honey. Blood sugar readings were then taken at 0,30,60,90, 120 and 240 minutes following ingestion a glucose tolerance test
Fructose showed minimal readings in blood sugar, which was consistent with other studies. Sucrose gave a higher blood sugar reading than honey at every time measurement.
The results showed honey provided the fewest symptoms of discomfort and as is it is sweeter than sucrose, fewer grams would be needed. We can therefore conclude it would seem prudent to recommend honey over sugar on a per gram basis because of the more gentler effect it has on blood sugar levels.