Let''s say I want to create a colour key effect such as that in directx and it''s evil ways, wherein, the colour I specify is my ''transperant colour'' and is not drawn as a part of my bitmap textures, how would I go about this (note: I''m using the glAUX library to load my bitmaps)

Take a look at Nehe tutorial on masking. You can also use alpha testing (glAlphaFunc)