to / too / two
except / accept
everyone / every one
into / in to
sometime / some time
maybe / may be
along / a long
(...etc.)
your / you're
conscious / conscience
brought / bought
sell / sale
were / where / we're
no / know / now
coop / co-op
rouge / rogue
yea / yeah / ya / yah
yay / yea
jive / jibe
defiantly / definitely / definitively
here / hear
there / their / they're
bare / bear
peak / peek / pique
our / hour
lead / led
tough / though / thou
trough / through / threw
who's / whose
whooping / whopping
costumer / customer
elude / allude
site / sight / cite
it's / its / is
comprise / compose
tweek / tweak
cue / queue / que
weary / wary
let's / lets
quiet / quite / quit
flack / flak
loose / lose
looser / loser
chose / choose
sweat / sweet
fuzz / fuss
tone / ton[ne]
add / ad
discomfit / discomfort
phase / faze
supper / super
breath / breathe
cloth / clothe
trooper / trouper
canon / cannon
decent / descent
reign / rein
vane / vain / vein
hone / home
reticule / reticle
dessert / desert
given / givin'
low / lo
loathe / lo[a]th
stationary / stationery
ones / one's
(and, more generally: [noun]s / [noun]'s / [noun]s')
crush / crash
brake / break
chic / chick
funny / fun
methodology / method
this / these
resign / re-sign
adverse / averse
complain / complaint
shoe / shoo
psyche / psych
then / than
common / come on
discrete / discreet
plane / plain
alter / altar
flare / flair
tow / toe
bias / biased
prejudice / prejudiced
hype / hyped
hoard / horde
canvas / canvass
dice / die
moral / morale
cant / can't
stratagem / strategy
compliment / complement
paddy / patty / Pattie
write / right
notch / nock / knock
boldface[d] / bald-faced
pick / pic
enlist / list
siege / besiege
statue / statute
dual / duel
glean / glance
weather / whether
tenant / tenet
prophecy / prophesy
wreck / wreak
feint / faint
laying / lying / laid
wont / won't
genera / genre
nit / knit
predominate / predominant
eek / eke
arch / arc
roll / role
"mid-evil" / medieval
do / due
bugged / buggy
hi / he / hee
specially / especially
vice / vise
fair / fare
set / sit
poll / pole
of / have
rite / right
diffuse / defuse
off / of
Indy / indie
pour / pore
shear / sheer
barley / barely
boarder / border
lightening / lightning
Gollum / golem
none / non-
advise / advice
council / counsel / console
enormity / immensity
prize / price
principal / principle
hung / hanged
improve / improv
reticent / reluctant
illicit / elicit
seder / satyr
waste / waist
cause / course
foot / feet

You're all welcome. : ]

EDIT: Removed duplicate
EDIT 2: Added words to a handful of existing pairs, and made some other, more minor tweaks