I have been able to eliminate the 1st to 2nd gear clunk most of the time by adjusting my clutch timing and lentgh of pull depending on how easy or hard I am accelerating. Brisk clutch and shift action above 4500 rpm almost always eliminates the clunk too.
This also happens to me when down shifting but I say "loud grears save lives!"
As Don illustrated in post #2, technique is important.
As for upshifts: instead of pulling in the clutch and then moving the shift lever, I pull in the clutch lever at the same time I'm putting upward pressure on the shifter. As the clutch plates disengage, the driving force through the transmission (which tends to keep the shift dogs engaged) reduces, and the box slips into the next gear. I aim to shift with the clutch lever pulled only halfway, and almost always succeed.
Don't chop the throttle as you shift up. Rolling off the throttle only a little makes the clutch reengagement after shiftiing much smoother. On my bike, even when in good tune, closing the throttle causes the rpms to drop precipitiously; even bikes with better FI than mine shift more smoothly while maintaining some throttle opening. I'll probably get flamed for this, but on city streets, I often make the 1-2 shift at 2500 rpm or less.
As to downshifts: you'll need to pull the clutch level all the way. Because the lower gear requires more revs for the same speed, you should slightly open the throttle as you downshift. With practice, I can now shift down smoothly and silently into any gear. No clunks! I enjoy the finesse, and I'm sure it's easier on the machinery, too.