As some have said above, if you're writing in third person POV, deep penetration, you don't need to indicate when the character is thinking -- everything on the page is coming to the reader through his senses and thoughts, painted or skewed by his emotions and intellect.
All third person POV need not be deep penetration. There might be times when you don't want the reader in the POV character's thoughts, when you might want more distance from him or her. Examples: You don't want the reader knowing what the detective knows as he surveys a scene; you don't want to probe the mind of an antagonist and reveal all his wicked plans. In this case, the thought attribution problem wouldn't even come up.
First person POV, same as third person deep penetration. Anything thoughtful on the page is coming from the POV character, so no need to label it as such.
In omniscient POV, where the author-narrator is jumping from head to head in a single scene, I imagine that thought-attribution would be necessary: Indeed, gentle reader, Barry thought that Mary was quite the eyeful. Unfortunately Mary thought that Barry was strikingly like a slug.
I wouldn't use quotes to set off thought -- that could confuse them with speech. I would only use italics to set off an unusual sort of communication, like telepathy. It seems that telepathic conversation in italics has become conventional in SF; it's a trick that works well.