Rule of thumb, Thule looks better, has nicer designs, maybe a few neat features, but can cost roughly twice as much and take twice as long to install than Yakima.
By neat features I mean some little things. I've come across very few Yakima boxes that can be opened with one hand. Something you don't think about until you're wrangling a bunch of gear, or a kid, while trying to load up the car. Thule is nice there.
If it's something you'll be taking on and off a lot though, Yakima's mounting brackets areusually fixed in position, which makes them easier to install. Some prefer Thule since you can adjust them, especially if you want to try and put another bike or ski rack on the roof.
Can't really go wrong with either, I've always just gone with the best deal I can find on kijiji and never been disappointed. Nice thing about roof boxes is so many people use them once or twice, then they collect dust in the garage until sold. Cheap and barely used.
Never used any other brands myself, just those two
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