If you have tons of links in your navigation it may be helpful to use tools such as CrazyEgg or ClickTale to determine which of your links are actually being used. If you present the user with too many options, they can often be overwhelmed and take no action at all. If a link is in the sitewide navigation but isn't actually getting any clicks, remove it.

If they don't have a physical address, they're not going to show up in Local Search (Craigslist/Angies List don't either).

Your best bet is to follow standard SEO practices and build good links & content. Create pages your site focused around each of the cities you are targeting, and make sure city name & zip code are in the URL, title, etc. Same thing for the individual business listings.

For on-page optimization, you can copy a lot of things Angies List is doing as far as SEO. For backlinks, get links from relevant local sites like local businesses, government websites, business associations, local news, etc.

Honestly, none of these URL structures is going to have an impact on your rankings, but my preference would be for www.website.com/apples?page=2.

The more important thing is to make sure that you have your canonical tags and rel=next/prev implemented properly.

Do not nofollow your social media profiles.

Adding nofollows to links does not increase your PR, it just eliminates the link juice that would have gone to those pages. Do not nofollow your own links or links to properties you manage. Only nofollow links if they are low quality sites, you have a commercial relationships with them, or they are competitors.

Linking to your social media profiles will also get them ranking higher in the search results for your brandname, which is a good thing if you maintain good social media profiles.

Brand new sites do not have any PageRank, therefore getting a link from them will not pass any link value to you. If, however, you plan on building links to those new sites, then the value of the link from that site can improve over time.