Micro-meteorites are small and can move very fast. It's like your ship being shot with a rail gun.
The cloud of particles isn't a bad idea. They can be charged particles if you like. Stars can spit out some pretty weird stuff.
Radiation: Even seemingly innocuous gas giants can generate some very odd radiation that could impact a crew negatively.
Dark matter is most likely the very stuff of which you are made. A poetic name, but all it really means is that it's matter that doesn't glow. Older theories allowed it, but more modern thinking is that most of the universe is not incandescent gas (i.e. a star). We used to think the sun was most of the mass in the solar system, but that was because we couldn't detect most of that mass with older equipment.
Space junk. The area around Earth is littered with fast moving garbage that we've left there. Similar to the micro-meteorite idea, but with the added don't litter message. Even water is litter in space because it turns into ice that can smack into other travelers.
Black holes are always fun, but they would be detectable long before you passed the no-escape zone.