He that touches pitch shall be defiled therewith.
(Ecclesiasticus Chapter XIII Verse i)

When I first came across http://www.morellibassoon.com/tuningcd.html   , I sighed deeply and muttered something unprintable about Americans. How earnest they can be! From this web site you can order a bassoon intonation CD. (a WHAT?) Just imagine hordes of over keen bassoon students religiously sitting in their living rooms playing long notes in unison with the CD. But this is not the point. This CD can be used in conjunction with a tuning machine. You will need to use a contact microphone to connect your instrument to the tuner.
Now let's get the CD playing, for example, middle C. Shut your eyes; play any C: listen till it sounds in tune; open your eyes and, surprise, surprise, the needle on your tuner is in the middle.
Play tenor G or F in the bass clef (so as to make a perfect fifth) and the reading will also be where you'd expect it (well, almost).
Now let's move on to thirds and sixths: eyes shut again; play a tenor E and get the chord to sound resonant and warm. You might be able to hear the 'resultant' (the low note that is generated when two higher notes are played together also known as a Tartini tone) which should be a low C. [There is a detailed web site on resultants or interference beats at http://www.phys.unsw.edu.au/jw/beats.html]. Now open your eyes and see how far the needle is from the centre and in which direction it is deflected. For many who are not sure what to expect, this can be a true epiphany - a revelation that that will revolutionise your playing for evermore.
Now let's try the same with a high A (the resultant should be a low F) a middle A flat (resultant: A flat below the bass clef) and a tenor E flat.
Because of the complicated mix of overtones on a bassoon, it can be difficult to get some of these two-note chords to 'gel' as well as some others - but don't worry about this. Then try this out on various different notes on the CD.
In the early days of tuning machines, many were able to generate notes as well as monitoring them and if you can get hold of one of these, you won't need this CD. Some of the more expensive tuners available to-day can still do this. One advantage of the CD is that, when using it, you can control the volume. One word of warning: wait till there is no-one else in your house or flat before you do all this or you'll drive them mad.

I remember when I had my epiphany. I was at a lecture given by the highly respected English flute player and teacher Trevor Wye ( http://www.trevor-wye.com/   ) who rigged up a big sine wave generator and a flautist wired up to a big pitch meter. The flautist 'bent' her note till we all agreed that it sounded in tune and then the reading from the pitch meter was shown to us.

There is some detailed information on different temperaments at  http://www.vibrationdata.com/piano.htm .

One advantage I have in my position as second bassoon in an opera orchestra over my colleagues in symphony orchestras is that very often the orchestral parts are 'double' parts (i.e. first and second parts printed together) so it's comparatively easy to work out what the harmonies are and therefore which way, if any, I should be 'bending' my note.
A word of warning here about leading notes (the seventh note in a scale): you might hear people talk about sharpened leading notes; this refers to the raising of the note by a semitone. For example, in the key of G minor the leading note is often F sharp not F natural but that F sharp should still be played to sound in tune within the chord (as likely as not to be a major third above a D natural).

People can get very worked up about intonation. My advice as a second bassoonist is to talk about it as little as possible. Generalised comments like 'so and so always plays sharp' are counter-productive and best ignored, hence the warning at the beginning of this entry taken from the book of Ecclesiasticus in the Apocrypha.

In much the same vein, Long John Silver in Robert Louis Stevenson's 'Treasure Island' says: 'You can't touch pitch and not be mucked'.