I went through the calculations myself last year. I opted for 1099, and haven't regretted it yet.
Firstly, you'll run into some fixed costs for going 1099. I became an S-Corp, so that could run you from a couple hundred bucks (internet) to maybe $800 (lawyer). Accounting fees will run me $1,000-$1,200 per year.
For me, the biggest thing was the solo 401k with profit sharing. I'm giving myself a salary of $72k per year with 25% match from the corporation. So my personal 401k is limited to $15,500 per year, and then I get $18,000 per year as profit sharing from the corporation. So that's $33,500 per year into my 401k, hosted by Fidelity. The remainder of the money comes to me in distributions.
Paperwork is kind of a pain, since I do that myself. I have to do my 2nd quarter 941 form in the next few days (and, irritatingly, a lot of stuff is on my computer whose power supply just went poof). If you don't want to do it entirely yourself, there are programs to help you out (~$20/month), or you could hire a payroll service, which for me would be on the order of $50/month. I used Quicken's online payroll service 3-month free trial to help me get started, then dropped that before the charges kicked in.
The real numbers do matter, though. Take $100k salary, $67/hr W2, $72/hr 1099. The overhead of payroll, accounting, employer payroll taxes is going to eat that $5 premium up quickly. You might still end up ahead if you plan on maxxing out the 401k. If you're at $150k, $100/hr W2, $108/hr 1099, you'd see more of a difference. Either way, the 1099 premium is fairly small. My premium is $7/hr, and that was enough to be worthwhile for me.
Salaried vs contractor is a whole 'nother barrel of fish. And that depends highly on the benefit package.