With just small changes you can make Arduino IDE better for your eyes. Try this, change theme.txt that is located in /Applications/Arduino.app/Contents/Resources/Java/lib/theme, dunno about Windows.

# GUI – STATUS
status.notice.fgcolor = #000000
status.notice.bgcolor = #54919e
status.error.fgcolor = #ffffff
status.error.bgcolor = #662000
status.edit.fgcolor = #000000
status.edit.bgcolor = #cc9900
status.font = SansSerif,plain,12

# GUI – TABS
# settings for the tabs at the top
# (tab images are stored in the lib/theme folder)
header.bgcolor = #216886
header.text.selected.color = #1a1a00
header.text.unselected.color = #ffffff
header.text.font = SansSerif,plain,12

# GUI – CONSOLE
console.font = Monospaced,plain,11
console.font.macosx = Monaco,plain,10
console.color = #000000
console.output.color = #cccccc
console.error.color = #ff3000

# GUI – BUTTONS
buttons.bgcolor = #044f6f
buttons.status.font = SansSerif,plain,12
buttons.status.color = #ffffff

# GUI – LINESTATUS
linestatus.color = #ffffff
linestatus.bgcolor = #044f6f

# EDITOR – DETAILS

# foreground and background colors
editor.fgcolor = #ffffff
editor.bgcolor = #000000

# highlight for the current line
editor.linehighlight.color=#005500
# highlight for the current line
editor.linehighlight=true

# caret blinking and caret color
editor.caret.color = #FF00FF

# color to be used for background when ‘external editor’ enabled
editor.external.bgcolor = #c8d2dc

# selection color
editor.selection.color = #888888

# area that’s not in use by the text (replaced with tildes)
editor.invalid.style = #7e7e7e,bold

# little pooties at the end of lines that show where they finish
editor.eolmarkers = false
editor.eolmarkers.color = #999999

# bracket/brace highlighting
editor.brackethighlight = true
editor.brackethighlight.color = #FF0000

# TEXT – KEYWORDS

# e.g abstract, final, private
editor.keyword1.style = #00FFFF,plain

# e.g. beginShape, point, line
editor.keyword2.style = #00FFFF,plain

# e.g. byte, char, short, color
editor.keyword3.style = #FF00FF,bold

# TEXT – LITERALS

# constants: e.g. null, true, this, RGB, TWO_PI
editor.literal1.style = #5599CC,plain

# p5 built in variables: e.g. mouseX, width, pixels
editor.literal2.style = #00FFFF,plain

# e.g. + – = /
editor.operator.style = #00FFFF,plain

# ?? maybe this is for words followed by a colon
# like in case statements or goto
editor.label.style = #7e7e7e,bold

# TEXT – COMMENTS
editor.comment1.style = #7e7e7e,plain
editor.comment2.style = #7e7e7e,plain

# LINE STATUS – editor line number status bar at the bottom of the screen
linestatus.font = SansSerif,plain,10
linestatus.height = 20