Best ways to write thoughts in narrative [closed]
Solution 1:
As @tchrist said, thoughts can be in italics. If you don't use italics, or quote marks (which I wouldn't advise) then you do need the "thought John" tag, or else it sounds like the thought of the author rather than the thought of the character. But having done it once, the tag will carry over by implication to succeeding sentences, providing they occur soon after.
The detective paused for a moment. He wants to know where I was yesterday, John thought. He's testing my alibi. Problem is, I haven't got an alibi...
In a scene where the point-of-view is firmly with one particular character, we've been dipping in and out of that character's thoughts often enough already, so you could dispense with the "thought John" tag, but you'd need italics.
"Are you familiar with the Parkside Bodyshop?" said the detective. Hell, he knows about the car!
At other times you could express someone's inner thoughts less directly. Rather than say "He's trying to set a trap, thought John" you could have "John knew the detective was trying to set a trap".
Just mix it up, is my advice. Too much italicising becomes a bit intense after a while, a bit shouty. Vary the volume by using all the different ways of tracking someone's thoughts.
Solution 2:
There are several different approaches to expressing thoughts, and no authoritative answer - or, rather, several, conflicting, authoritative answers.
Undecorated thoughts - no quotation marks, no tags, no italics; just a change in tense and/or person - are recommended by people who argue that the most important thing is to avoid breaking up the flow of the text. Sometimes it's sufficiently clear that something's a thought rather than narration, and you don't need to advertise the fact.
Italics have been popular - I've seen informal surveys of recent literature conclude that they've fallen out of favour - they offer the advantage of clearly setting thoughts apart from both dialogue and narration without the need for tags, but they conflict with the use of italics for emphasis, and large amounts of italicised text gets tiring to read. Also, while you generally shouldn't be switching between multiple characters' thoughts that quickly, if you do have consecutive thoughts from two different characters, you'll probably need to do more to distinguish them since there's no way to tell whether the intervening white-space is italicised or not (unlike speech marks). Also, electronic displays sometimes either have trouble displaying italics, or fail to stop italicising text at the intended point, either of which can destroy your careful formatting.
Tagging thoughts is another option (sometimes combined with use of italics) and certainly works, but, just like tagging speech with "he said", it's best to keep the "he thought" tags to a minimum, and only use them when they're needed to help keep track rather than tagging every single time.
Using speech marks for thoughts is sometimes advocated, but, as mentioned in the question, it means speech and thoughts can get confused for each other. Personally, I find the argument that speech marks should be kept for actual dialogue persuasive.
If (but only if) you include a lot of thoughts in your narrative, and it's important that they be immediately distinguishable from the narrative around them, then inventing your own notation (or stealing it from someone else) is an option - SF&F stories with telepathy, or stories featuring someone with multiple personalities interacting internally have used assorted conventions to indicate thoughts, but you do need to justify the reader taking the time to learn your novel convention rather than using a more conventional one.
Finally, rewriting to either report the thought indirectly, or to imply it, rather than presenting it verbatim, eliminates the need to decide how to present it. Decide whether you really need to embed the thoughts in the text directly.
Whichever approach you pick, once you've decided how to represent thoughts in your narrative, it's best to stick with it - switching between notations without a good reason will just confuse your readers.