"Don't be tired" is odd - not because of the grammar but the meaning. If you're tired than there's nothing you can do about it - you are, and that's that. So to tell someone
"Don't be tired" makes no sense. Notice it's not the grammar though.If someone is acting in a silly way, you could say for example -
"Don't be silly" , because they do have a choice - they can stop being silly if they want. But you can't decide to stop being tired. Instead, if this is the end of the lesson, then
"I hope you're not too tired" or
"I hope you didn't get too tired" would be appropriate.
"Well done" is fine as an expression - but would usually be used after succeeding at something really challenging. For example the teacher might say it to encourage a student who had got a difficult grammar point right or performed well in a roleplay. If a student said it to me at the end of the lesson I might get the feeling he was saying
" Thank goodness - at last you've managed to give a decent lesson" 
"Good job", again said by a student, might have the same implication - but it sounds odd to me anyway. If I used it to anyone, it would probably be in a longer sentence :
You did a good/great job there. I seem to remember it being suggested on this forum before, so said like that it may be an American usage. But in any case I'd suggest it's more appropriate T to S rather than the other way round.
"Teacher" - I cringe every time I hear this. Lots of languages use professions as titles - my students often use "teacher" as a translation of "Professoressa" which is what they would (very respectfully) call me in Italian. But in English we don't - we'd just use names - the first name if it was an informal situation (I always start my first class with adults with the firm instruction
Please call me Susan), and title + surname (eg Mr Brown, Mrs Evans) if it was more formal - in a school situation with kids, for example.
So what should the students say? Any of the following would be fine :
Nice/fun/interesting/useful lesson - thanks a lot. Thanks - that was a nice/useful/interesting/fun/good/great lesson
Thanks David - I enjoyed that lesson
Thank you Mr Brown - I found that lesson very useful
Hope that helps.