As other have mentioned, the Ortlieb roll-top duffels are great, and the POE zippered bags are very nice but not fully waterproof. SealLine Zip Duffles are duffle bags with a true waterproof zipper. However they're expensive ($120 and up). They also don't open as wide as the Ortlieb rolltop bags.

Both POE and SealLine make backpacks and bike messenger bags that are waterproof, in case a backpack style might work for you.

I'm still a fan of the usual tube rolltop. Not as convenient access, but fit in a lot of places, simple design, and after years of abusing several they've worked well.
J