All very interesting replies.
I agree with those who claimed that Charles' legacy as King would start when he becomes King. However I do see a way for his efforts up-to-date to put him in a better position to leave a legacy.
The issues that he has cared most about - the environment, alternative forms of energy - are now coming to the forefront of the general public's consciencenous. Right now because of gas prices, companies are seriously looking into alternatively fuelled cars. If this public attention is not just a fad but brings about some real change in how people lead their lives, then Charles could have been said to be on the forefront of a monumental change in public perception. It won't matter IMO whether he himself was instrumental in the change because people on the forefront get credit whether they played a major part or not.
If this new way of living becomes standard by the time he becomes King, then he can take steps to make Buckingham Palace more green and thus appear as he's just following in the steps of public opinion (ie, acting non-controversial) while all along people will know with Charles it won't be a public relations exercise because of his previous commitments.
Already because of the growing awareness of environmental issues, I've seen two non royalty focused articles that praise Charles for being ahead of the curve. No mention of his personal troubles was made in either article. That is not to say that people forgot his personal life, but it does appear for some that the environmental issue is important enough to focus on that entirely to the expense of his personal troubles.
If the number of people that care about this grows, Charles will become more relevant to the common man and the issue will become less and less controversial thereby letting Charles as King have greater influence.
Of course, as King, he will have to curtail his public statements but if the groundwork is already made, he won't have to say much.