Initial tuning notes are listed below for each instrument. Play your tuning note into the tuner. If the needle stays towards the right, your note is sharp. If it stays towards the left, your note is flat.

The LONGER the pipe, the LOWER the pitch. If your pitch is sharp (high), you need to make it flatter (lower).

The SHORTER the pipe, the HIGHER the pitch. If your pitch is flat (low), you need to make it sharper (higher).

Initial Tuning Notes for each Instrument (not transposed) - Keep in mind that even though you will learn how to tune these notes, other notes on your instrument may not be in tune. It is the nature of instruments. The longer you play your instrument, and the better tone you have, the more you will be able to play all notes in tune on your instrument.

Flute - A above staff (play F G A Bb slurred, then go to A and tune)
Oboe - A in staff
Bassoon - Bb in staff
Clarinet - open G (adjust barrel); 4th line D (middle joint)
Bass Clarinet - Open G
Saxophone - top line F# (play low G, C above that, high G, all slurred, then go to F# and tune)
Trumpet - 3rd space C, 2nd line G
French horn - middle C (if trigger, 3rd space C)
Trombone/Baritone/Euphonium/Tuba - Bb above concert F (play F first for reference)

For each instrument (except oboe and bassoon), you will move something on the instrument to make it longer or shorter, depending on what the tuner says. 

Flute - move the headjoint in or out to make the flute longer or shorter
Clarinet -  for open G, move the barrel of the clarinet up or down, then for fourth line D, adjust the middle joint of the body of the instrument
Bass Clarinet - loosen the neck screw, and move the neck of the instrument up or down to make the instrument longer or shorter, tighten neck screw when the neck is in the right position
Saxophone - move the mouthpiece up or down on the cork to make the instrument longer or shorter
Brass - move the tuning slide(s) in or out to make the tubing of the instrument longer or shorter
Bassoon/Oboe - put reed all the way onto instrument or bocal, then loosen lips to sound lower and tighten lips to sound higher