I'm keep trying to find difficult or complicated sentences that I don't know how to say in esperanto. Once I thought that I would be able to say almost everything once I understand the structure, but yeah, I was being naive. :q

I'm not demanding full-translations. Just, if you know how to say one of these and if you want please share your knowledge.

Sentences that I don't even have a clue.
- All I want is for you to be free.
- What if she don't want all these?
- That is only if you tell me what we're after.
- You'd better not say nothing to her.

Sentences that I'm little confused about.
- Shouldn't John have been nominated as the best employee of that month?
(devis? devus? Which one is correct in this case?)
- Could you make it seem to be separately deposited several times?
(Is it correct to say 'Ĉu vi povus fari ŝajni ke ĝi ~'?)
- What you should've done was just leaving them back there.
(Can we say 'Kion vi devis fari estas ~' instead of 'Vi devis ke~'?)
- The smell of boiling noodles is good.
(Can we say 'la odoro de boligi nudelojn' instead of 'la odoro de boligata nudeloj'? I want to focus more on verb(boiling), not the object for it.)
- Take me to a place where nobody knows.
(Do I have to use 'kien' (~neniu scii) on this? It's a place but seems to be used as an object in the sentence just like 'Nobody knows it'.)

Here are some suggestions. Different people will have different - equally good - solutions.

All I want is for you to be free - mi nur volas ke vi estu libera (or) mi volas nur tion, ke vi estu libera.

What if she don't want all these? - Kaj se ŝi ne deziras ĉiujn ĉi? (and if she doesn't want all these?)

That is only if you tell me what we're after. - sed nur se vi diros al mi, kion ni serĉas. (but only if you tell me what we are looking for)

You'd better not say nothing to her. - vi diru nenion al ŝi (or) estas konsilinde ke vi diru nenion al ŝi (you should say nothing to her; it is advisable that you say nothing to her)

apriliss:
- Shouldn't John have been nominated as the best employee of that month?
(devis? devus? Which one is correct in this case?)

I would say: ĉu ne estus dece ke John estus nomumita kiel la plej bona dungito ...? (wouldn't it have been appropriate that John would have been nominated ...)

You could use "devi" but you would need a complicated phrase such as "ĉu John ne estus devinta esti nomumita" (shouldn't John have had to be nominated). That looks and sounds clunky in Esperanto, and "clunkiness" is often a hint that there is better way of expressing the idea that is more in harmony with the look and sound of our language.

- Could you make it seem to be separately deposited several times?
(Is it correct to say 'Ĉu vi povus fari ŝajni ke ĝi ~'?)

ĉu vi povus ŝajnigi ke ĝi estis aparte deponita plurfoje (could you make it seem as if it had been separately deposited several times?)

- What you should've done was just leaving them back there.
(Can we say 'Kion vi devis fari estas ~' instead of 'Vi devis ke~'?)

tio, kion vi estus devinta fari, estis simple postlasi ilin (what you should have done was simply to leave them behind)

- The smell of boiling noodles is good.
(Can we say 'la odoro de boligi nudelojn' instead of 'la odoro de boligata nudeloj'? I want to focus more on verb(boiling), not the object for it.)

bolantaj nudloj bonodoras (boiling noodles smell good).
When they're bubbling happily away, that's "boli". To *make* them boil is "boligi": ni boligu iom da nudloj - let's boil some noodles.

- Take me to a place where nobody knows.
(Do I have to use 'kien' (~neniu scii) on this? It's a place but seems to be used as an object in the sentence just like 'Nobody knows it'.)

It would be helpful to memorise these two sentences:
la loko kie mi loĝas (the place where - i.e. *in* which - I live.
la loko kien mi iras (the place where - i.e. *to* which - I go.

"Take me to a place to which nobody knows" doesn't make sence, so you want "in which": konduku min al loko kie neniu scias