The 50D apparently has less DR than the 40D - according to DPReview - so accurate exposure is more critical. The noise is reckoned to be better, per pixel, on the 40D, but better on the 50D if you downscale the 15MP 50D back to 10MP (thereby reducing noise by multi-pixel resampling). For the most part, the differences are very small. Most should be explained by trying to boost shadows (where the SN ratio is worse) or correcting an under exposure by boosting everything.
I've not had issues of noise in the ISO <=800 range with my E-3 (supposedly less good than the 40D or D300), which is helped a lot by the Zuiko optics being a bit brighter than their Canon/Nikon counterparts (e.g. in the 70-200 and standard kit range). This small difference is also massively helped by being able to get tack sharp pictures with the lenses wide open! Add in all lenses are stabilised (5 stops, not 2 or 3 or 4) by sensor-shift stabilisation, 11 cross-type AF and weather sealing that allows you to rinse your camera under a tap.... blah blah... etc. I've said enough...
I don't think there is a cheap answer to this, short of going back to the 40D or upgrading to the 7D. I have to say that the performance of the 300/4, as shown in the other thread from Sarah, is not very satisfactory, with or without a filter, and should also be investigated to see if there is something awry there (I don't think that is related to technique or exposure) - hopefully this isn't typical performance for the 300/4, with so much fringing and other issues.
Andy