I let the players roll usually (even spot and listen), but I make secret rolls sometimes, when something happens, which I do not want to alarm them about by anouncing a roll. This rarely happens, tho, since 'roll listen and spot, please' is just too common to know, if there is anything important happening, and if the players roll low, they usually do not begin to watch their surroundings with paranoia!
Also I let them roll on many occasions, where something completely unimportant happens to them, so the 'roll listen and spot, please' phrase is not as alarming as it might be.
Usually, when it is used to determine an ambush, for example, surprise round starts, after the roll is made, so there is no time to react 'to the roll itself by metagaming' anyways.
Again, if there is something, which they might notice, or when a skill roll is applicable (sense motive is one good example in this context, announcing a sense motive roll can give away a lot), and I do not want them to know anything about, I make the roll secretly.
Some skills (I already stated sense motive, disable device might be another one of these) are best handled by secret rolls, while most skills can be performed by the players themselves, as long as they do not heavily metagame (like that 'I rolled low on search, let's search again' example above - dude, use take 20 if you want to find everything!

).
So my answer is... depends!
Bye
Thanee