I'm in the process of going through a very similar upgrade from a 40D. I knew I wanted to go FF and similarly, had a $3000 budget. I already had 3 lenses (17-40L, 85 1.8, and 70-300 IS) plus a 430 EX II, so my needs were a little different, but here's what I ended up buying (it's currently in transit):
6D w/ 24-105mm
The 24-105 seems like such a versatile lens and comes at a deep discount in the kit. It was a no-brainer for me.
40mm 2.8 STM
I was looking at the 50 f/1.8 and 35 f/2, but decided to go for a solid build and newer lens in the shorty-forty, even though it's a at least a full stop slower.
77mm B+W Circular Polarizer
For landscape photography with my 17-40 and 24-105.
A bunch of accessories
The extras can really add up, especially if you have a firm budget. I added some cleaning supplies, memory cards, 2 extra batteries, a new bag, Syl Arena's Speedliter's Handbook. I also decided to get lens hoods for my 85 1.8 and 70-300mm.
I'd agree that a flash would be a good item to consider. I don't have experience with anything other than the 430 EX II, but it has greatly improved my photos ever since I bought it last summer. Another +1 for the 85mm 1.8 as well. It's been my favorite lens on crop and I hope it finds a lot of use on FF.
Also, you might want to take a look at your tripod if you plan on doing occasional landscapes. If your current tripod is a cheapie, you might want to consider an upgrade there as well.
All in all, I'm sure you'll be pleased with your new setup, whatever you decide!