I have a 2004 with 41k miles, it has developed a very strange noise... when in gear I get a noise ( Almost like the noise you got when you clipped playing cards to your spokes on your pedal bike !) ,or could be described as a flutter/ ticking noise. Only makes the noise when under load.when moving and I depress the clutch the noise stops, or when moving and I put the in netural it stops. Any clue ?? bearings . ? tranny problems ? ,dry half shaft ? Any easy things I can check beforeI cave and take it in tomy dealer? Noise sounds like it is comming front left side thxs

http://www.mini2.com/forum/first-generation-faults-fixes/165621-ticking-noise-1st-2nd-gear-neutral.html

Is this the same thing? Try a google search. Lots of ticking.

MINI Cooper R53 JCW Clicking noise during acceleration - YouTube

or this?

mine has much more of a "flutter" type noise,with no whine. I am thinking something is just loose and is banging around. Again it only happens when under load

just noticed that my muffler is in bad shape, one hanger in the very back is very loose, could that cause
the whole exhaust assembly to knock around ?

yep

If your Mini is a Cooper or One, what month was it built in 2004, see the label under the bonnet for build month, also pre or post-facelift model?
If it is a pre-facelift Cooper/One built before July 2004 then it could be the bearings going in the Midland gearbox/transmission.......they sometimes make a sound like a helicopter.

More details here:
Early MINI Rover Midland Gearbox - Forums (http://forum.minicooper.org/showthread.php?t=9643)