For a moderately priced acoustic, I think it's hard to beat a mahogany back and spruce top. The spruce is vibrant and loud, and the mahogany has a mellowing tightness to it. The sides at that price point probably don't make much difference.
The biggest step up of course is from a composite body and top to a composite body with a solid top (usually spruce). That's a huge difference. It happens around the $200 price point here (U.S.).
The next step up is to a solid back. I like mahogany, but spruce, koa, and other woods work too. That's getting into the $500 price point. Electronics and better woods are generally trade-offs in that price category.
I don't know much about guitars better than that, as I don't expect that I'll ever go much beyond the $500 price area for a guitar. Gretsch had a solid body with koa and mahogany that sounded real nice, but was pretty heavy. There are any number of guitars with mahogany back and sides with a spruce top in that price range. I think that's an excellent combination of woods.
As far as wood for necks and fingerboards, I'm out of my league. I couldn't tell rosewood from zebrawood from onyx by the sound. On my basses, one is onyx and the other is rosewood. I can't tell a difference. My electric is a rosewood fingerboard. I have no idea about my acoustic guitars. Rosewood seems to be the wood of choice in my price range. I would assume that's based on a combination of availability, suitability to purpose, ease of working it for the luthier, and price.
Of my basses, one of the bodies is solid mahogany (wonderful!) and the other is ash. The ash is nice and light. The solid mahogany is far from light, but MAN does it have sustain. I could hit a note with it on the wall, go cook and eat lunch, come back and have to mute it before playing the next note. My electric guitar is maple. It makes a good electric body, but I don't know about acoustic. I've seen flame maple acoustics before with 'bookmarked' patterns, but I think that's mostly for looks and not as much for sound. But what do I know? I'm no luthier.
- Zurf