I'm a big fan of the kelty packs. Between the pair of zippered side pockets, the huge top pocket, and the multi-compartment front pocket, you can keep things fairly organized. The internal hydration pocket is also useful if you're not using a hydration pack. There's also a pair of side mesh pockets that are good for holding energy bars and such. They can also hold nalgenes, but as you mentioned they can pop out when running or other sudden movement.

If you're looking for something the size of a daypack, the Serac is basically a mini version of the larger packs like RedCloud, with all the same features except the sleeping bag compartment, with the addition of small pockets in the stowable waistbelt( just the right size to hold a cell phone, leatherman, etc.). Kelty doesn't make the Serac anymore, but you can find it online.

I have the Serac, which I use for most everyday stuff, and the Redcloud 5000, which I use when backpacking or whenever I need to carry a lot of stuff. I actually find the Redcloud much more comfortable, because it has more support and a stiff waistbelt (the Serac has an internal frame, but the waistbelt is just fabric and can provide some stabilization, but not support.

The Kelty Serac: