But first begs pardon: even in executing someone, the executioner begs pardon from condemnation before letting the ax fall.

he: the executioner

Pheobe: Pheobe's response becomes a critique of the conventions of romantic (Petrarchan) love poetry

muder in mine eye: the eyes were thought to hold real physical power; this is also a Petrarchan common place

gates: eyelids

atomyes: specks of dust

counterfeit: pretend

darted: shot like arrows

as that ever may be neere: may the time come soon

power of fancie: ability to attract

Loves keene arrows: Cupid the god of love, was traditionally pictures with bow and arrows

As till that time I shall not pitty thee: Phebe is referring to Silvius' mention of the time that she will see the hurt that Love inflicts on someone's heart as it has on him. She says that until then, not to come near her, but he can mock her when that time comes without pity, since until that time comes, she will not pity the pain he currently feels from his love for her. This is foreshadowing the next moment when she will see the hurt that her Love for Ganymede can inflict on her own heart and the time she is referring to arrives sooner than she predicted.

who might be your mother: Rosalind is implying that Phebe's unkind behavior must be inherited or bred from her mother; she's basically saying, "who raised you?" and insulting Phebe.

Then without Candle may goe darke to bed: who are not even attractive in the darkness; compare the proverb "when candles be out, all cats are grey"; No man who had to look at Phebe would want to put his Candle (penis) into her darke (female pudendum, cunt), indeed no man would go to bed with Phebe unless "by candle light."

entame my spirits: literally subdue my spirits; also entame (castrate, make impotent, effeminate) Ganymede's spirits (genitals and semen).

South: the south wind; Phebe is puffing (swelling with anger), and Silvius' judgement is made foggy by her rain and wind; Silvius is also under the raine (ruling, power) of his raine ("rein", kidneys and loins regarded as the seat of sexual desire). Thus he is puffing (has an erection, to swell/bulge) and desires to winde (copulate). 

properer: more handsome

full of ill- favoured children: i.e. by marrying ugly women

glasse: looking-glass; Rosalind also hints that Phebe is a "piece of shit" who would have no trouble finding a likeness of herself in a glasse (chamber-pot, toilet).

lineaments: facial features

Mistris: innuendo being whore, wanton, prostitute

you are not for all markets: you're not everybody's choice; proverb: "As the market goes, wives must sell"; Phebe's market (vulva) would not be very desirable for market (copulation) even if available on the market (were she a prostitute).

Cry the man mercy: beg him forgiveness

Foule is more foule, being foule to be a scoffer: foulness is more foul when it consists in being scornful; implication that Phebe is a "fowl" (wench, whore)

chide: scold

in wine: intoxicated

tufft: clump; Olives are a symbol of peace so Ganymede may be indicating he has no interest in Phebe's tufft (pubic hair and vagina).

here hard by: nearby

ply her hard: persist with her; Silvius should ply (woo) her to ply (have sex with) her.

abus'd in sight: deceived by what he sees; also implying he is abus'd (screwed, used of illicit or unlawful sexual acts) of his sight (anus, a "site" is literally a "seat").