Here's a site that should explain this reasonably.
http://library.thinkquest.org/16020/data/eng/text/education/theory/ensemb.html

Written and sounding are two different puppies. Remember, the guitar is written 1 octave higher than it sounds. The open A (5th string) is the actual concert 440. Guitar is considered a C instrument. Like a piano, flute, fiddle, etc.

Brass, horns, saxes, harmonicas and certain winds are tuned. It's the nature of the building of the instrument.
Length of pipe, valves, reeds and such. Most people can't afford differently tuned instruments, so a standard arose.
Bb, Eb and F instruments are where they are. Their world is only Bb, Eb or F. They themselves transpose or are transposed (written) to C instruments or concert pitch.

Depending on instrument range the standard is this:
Bb = write a M2 above concert (the key of the tune)
Eb = write a M6 above concert
F = write a Perfect 5th above concert.
Trombones are written in C (or concert standard) in traditional music. (classical) But in brass bands, marching bands and some jazz bands, bones are written as a Bb instrument.
I hope this makes this clearer. This can be horribly confusing. If you have cakewalk, this idea can be heard in midi format.