BY

By is used to indicate proximity. Example:

Can I sit by you?

He was standing by me.

The post office is by bank.

By is used to indicate the person that does something in a passive voice

sentence. Example:

The microwave was fixed by mechanic.

The flowers were delivered by postman.

The branch office was closed by head office.

By is used to indicate an action with a particular purpose. Example:

You can pass the exam by preparing for it.

I expressed my feeling toward her by writing a letter.

She finally broke the record by pure effort.

By is used to indicate a mean or method. Example:

Please send this package to Russia by airmail.

I came here by subway.

We use by to talk about a deadline when something will happen before that time.
Example:

By tomorrow

By next week

By six o'clock

By Wednesday

By summer

By is used to show the person or thing that does something. Example:

The motorcycle was driven by tiny bald man.

I'm reading some short stories by Chekhov.

I felt frightened by anger in his voice.

By is used to show how something is done. Example:

1

They travelled across Europe by train.

He learned English by listening to the radio.

I refuse to live by their rules.

By as a preposition is used to express near or at the side of. Example:

A small child stood sullenly by her side.

He wanted to keep her close by him always.

The policewoman walked by them without saying a word.

By is used to show measurements or amounts. Examples:

Our office floor space measured twelve meters by ten.

Their wages were increased by 15 percent.

Freelance workers are paid by hour.

These phones have sold by thousand (= several thousand have been sold).

By is used to say that something increases or changes with every minute, hour,
day, etc. Example:

The death toll from the hurricane was climbing minute by minute.

The credibility of the campaign has deteriorated month by month.

By is used to describe or show what happens every minute, hour, etc. Example:

A minute-by-minute timeline of the incident.

The book paints a detailed, week-by-week portrait of his father's illness.

By is used when describing someone's character, job, etc. Example:

She is, by nature, a sunny, positive kind of person.

He's a plumber by trade.

She was, by profession, a lawyer.

With
Used to indicate "using":

eat with a fork; made us laugh with his jokes.

I wrote a letter with the pen you gave me.

(talkenglish.com s.f.)
BESIDE
Is used only as a preposition, which means there is always a noun following it. It
means either next to or compared to, as shown in the examples below. The
first meaning, next to, is more common.

She sat beside (= next to) him during dinner.

I like to sit beside my friend.

(Mairs s.f.)
Bibliography:
Mairs, Jane. Meriab Webster. s.f. http://www.learnersdictionary.com/qa/differencebetween-beside-and-besides-preposition-adverb (ltimo acceso: 14 de
Enero de 2016).
talkenglish.com. s.f. http://es.talkenglish.com/grammar/prepositions-with-overby.aspx (ltimo acceso: 14 de enero de 2016).