My HDV footage is 1080i and my DSLR is 1080p, but the biggest issue is that my HDV footage is 30 fps and my DSLR is 24 fps at 1080p or 30 fps at 720p.

What is the best settings for both cameras to get the best overall footage when mixing these clips to create a final for the web? 99.5% of all my videos are for the web.

I'd match the FPS on both camera's.
Depending on what software you use for post, it should handle the Interlace issue easily.

FWIW, mixing DSLR and one to three camcorders and or GoPro, is SOP for me. I'm a one man show and often have two camcorders on tripods with the DSLR on a shoulder rig and often, a GoPro hanging on me somewhere.

It works out in the end.

Don's right: Make sure both cameras are set to the same frame rate. I'm currently working on a project where I need to mix video from a Canon 7D, a Canon T2i, and my Sony HVR-V1U. The video from the DSLRs tends to be slightly sharper on account of them not having anti-aliasing filters in front of the sensor like a video camera has. Also, the color you'll get from each camera will look different. Make sure you white balance both cameras at the same time. If your shoot is going to take more than a couple of hours, you'll want to white balance each camera a few times over the course of the day to keep color discrepancies to a minimum.

When your project is all finished, you can render out as 720p or even 480p to get rid of the most glaring differences.

Thanks guys, I figured that frame rate was going to be an issue... Hopefully Nikon will have a firmware update with the ability to shoot 30 fps at 1080p.

Color is going to be fun to try to match.

I love the white balance tip, I have Warming Cards that I will use to match the to bodies.

Chris what about the d7000?