I would agree with others that Samus does well against Ness. Her uair cancels Ness' up b when getting juggled, missiles are actually good against him, he struggles really hard getting through zair/ftilt/utilt/nair, can't combo Samus very well, and like a lot of other characters are able to do, Samus can gimp him well. Ness' up sides are the typical ones he has, air dodge and bthrow among other things. Depth has great results against Florida Ness players, I might even be inclined to say Samus has an advantage in the MU. Samus does well against most slow characters who can't break her zoning, like Luigi.
Her MUs against Peach, DK, and Ryu are good, for similar reasons that she does well against Luigi and Ness, they struggle to get in. It sounds like a simple/not good enough reason, but that's the argument Luigi mains used to make (and probably why their MU thread has Luigi beating Samus 65:35...), but it's actually pretty bad for the opponent. I haven't seen a whole lot of Ryu vs Samus, but by what I have seen/my own experiences, I can't see it being worse than even. Looking at MUs Ryu struggles with, like Mega Man, I wouldn't be surprised if Samus actually has an advantage against Ryu, since Mega and Samus do well against similar characters for similar reasons.