Send your best pages, whether they are cover or inside pages. Do no feel compelled to include a jump page because you send a cover. I'm in a position now where I hire designers, and unless they did something awesome with the jump page, I don't care about it. I assume a designer who laid out an awesome cover can handle a jump page. And if not, I'll figure that out later in the process.
However, I'm also impressed if someone does something cool with inside pages, like game previews or such. If you can show a good hand at treating inside pages as well as front-page packages, it can only help you.
And Mark2010, you're wasting time sending the whole section. Maybe other papers are different, but I just want to see a handful of pages that wow me. Until recently, I did almost all sports, and unless you're doing something amazing with your agate, it isn't going to wow me. Maybe impress slightly, but it won't wow me. It's agate. I used to take a lot of time on agate, too, and I would NEVER have sent an agate page. Maybe if it's a job where you'll be doing both writing and design, they may look through it, but if I ask for 4-6 samples, I want 4-6 pages. I go through them the first time, and if they don't catch my attention, they go into the discard pile.