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I don't (read can't) answer a lot of questions, but I do ask some questions. Nothing makes me want to say "thank you" like a quick answer that gets me out of my jam. I feel the need to thank the person, but I know that's discouraged in the comments. But maybe for the answerer they don't care and an upvote and question acceptance is all the thanks they need.

So four psychological needs are at play here from askers and answerers: askers who feel a need to thank and those who don't, answerers who appreciate thanks and those who don't.

If thanks, are in order, but not necessarily desired to record permanently, some functionality where when you accept an answer a pop up box comes up that says "Say thanks or leave a useful comment for others" with a radio button to choose one or the other (and a 'skip' option). Thanks goes straight to the answerer and isn't recorded permanently, comment goes under the answer.

If the majority of people just want reputation, then I would suggest a slight change in wording for the comments instructions. Something like: "Avoid comments like "+1" or "thanks" (an upvote is all the thanks we need!)"

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Jon Skeet claims he's about gratitude, but I don't believe him. – Cole Johnson Sep 28 '13 at 1:44
We will never know. – Pëkka Sep 28 '13 at 1:46
@ColeJohnson: Jon Skeet can turn gratitude into reputation. – Jamal Sep 28 '13 at 1:50
@Jamal Jon Skeet is reputation. – Cole Johnson Sep 28 '13 at 1:51
I for one prefer interesting, high quality questions. I am in heaven when askers put an effort into making their question as good as possible. Can't tell what text in comments is needed for that – gnat Sep 28 '13 at 5:42
No ones really going to blame the original question OP for saying thanks in a comment, its when everyome chimes in that it becomes a problem. Consider deleting your own comment after you know the other person has seen it – Richard Tingle Sep 28 '13 at 5:45

If you just mean "thanks, that was it, appreciate it" then the +25 is a synonym for that.

True story. I worked in a building where the elevators had visual sensors to make sure the doors didn't close on you. When you walked into the elevator it made these little click sounds as you passed the sensor, even if the doors weren't trying to close. Sometimes I had to visit another building and I noticed I was always grumpy as I got to my floor in that building. Eventually I realized it was because the elevators there did not acknowledge me. Somehow I had that little mechanical click mapped to "hello" and it bothered me not to get it. In the same way +25 is firmly mapped to "thanks", +10 during the first few days of a post to "you got it, that's right, good job helping the asker", and a years-after-the-fact +10 is mapped to "just came across this and it was what I needed, appreciate that."

If you mean "oh my gosh thank you so much I was stuck for an hour and then after I got it working everyone was impressed and I really feel I get the concepts better now and by the way did you write that book I really liked, I can't believe I got an answer from someone who wrote an actual book I'm going to buy all your stuff from now on thanks again" then do feel free to say it. I for one appreciate reading enthusiastic gratitude and I expect I'm not alone.

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This made me realize how important small things, which might annoy you at first, can become. Thanks! – 3ventic Feb 22 '14 at 0:09
In this case please map "+10" to "the elevator story brightened my day" – Richard Tingle Feb 22 '14 at 10:29

It seems like up vote and checking it as the answer is not only saying thanks, but giving them a reward. It would be nice tho if you could add a small comment when you check off an answer that shows up only in answerer's inbox.

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+1 thanks (an upvote is all we need) – Cole Johnson Sep 28 '13 at 1:45
+0.5 for the answer and another +0.5 because I love decimals! – Jamal Sep 28 '13 at 1:57
@ColeJohnson: I've actually seen such a comment (minus the specific reasons) used before, presumably in a very enthusiastic manner. That's why I used it. I know you're correct. :P – Jamal Sep 28 '13 at 2:02
@ColeJohnson: If you're using any sensible kind of binary floating point type, then you can absolutely rely on 0.5+0.5 being 1. It's not like 0.5 is hard to represent in binary. – Jon Skeet Sep 28 '13 at 6:44
@JonSkeet I know 0.5 is 0.1 (or 1.0 x 2^-1) in binary. I was making a joke. -_- – Cole Johnson Sep 28 '13 at 17:55
@ColeJohnson: I realized it was meant to be a joke - I was just pointing out that it was unfortunately inaccurate (unlike the binary representation of 0.5). – Jon Skeet Sep 28 '13 at 18:17
Ugh, a comment that shows in the answerer's inbox? I try to cut down on spam. – Gilles Feb 14 '14 at 4:02

All I want is your gratitude!!

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Thank you for your answer! – Jamal Sep 28 '13 at 3:26
That's all I really wanted. – jonsca Sep 28 '13 at 3:26
+0 thanks! okay kidding.. upvoted. – chue x Sep 28 '13 at 4:15
-1 I don't like your gratitude. – Cole Johnson Sep 28 '13 at 19:03
+1 just to share – Shadow Wizard Nov 26 '13 at 14:58

If the majority of people just want reputation

Then those people should probably get a job where they get paid and leave the SE network behind.

I feel the need to thank the person, but I know that's discouraged in the comments.

Not really. I think that was put there to discourage a bunch of unneeded comments where everyone that it helps puts "Me too", "that really helped". That's fine from the asker and I think actually encouraged. The rep is great but I also encourage a little ego boost of, "Thanks for your time", especially when I have put in more than "normal" time and effort in on a post. But if you aren't the OP then an upvote is thanks enough unless you have a bit of information to add to the post.

On the same token, I don't get upset if someone doesn't leave a comment as long as they have the courtesy of accepting and/or upvoting.

If thanks, are in order, but not necessarily desired to record permanently, some functionality where when you accept an answer a pop up box comes up that says "Say thanks or leave a useful comment for others" with a radio button to choose one or the other (and a 'skip' option).

I think this is unnecessary overkill. Just say thanks...I promise you won't be banished!

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I do it for the people who need help - the ones asking the question.

Both of my parents were teachers, and I too find joy in educating others. I myself spent a couple semesters teaching at a university. Didn't pay great, but it's incredibly rewarding just to watch people learn.

As to your specific question, upvotes and accepts are ways of showing gratitude, so I think of the two as one and the same. That being said, I prefer reputation over comments because comments add clutter to the site.

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I think people who give the best answers don't do it for the Reputation they can earn. And an upvote is a fine expression of gratitude and see it exclusively as a reputation reward simplifies the question too much.

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