Theoritically: none (this is what Robin Shields stated twice) At Laphroaig they claim there are no differences between the old Straight from the wood and the new Cask Strength bottlings.
Practically: lots! For starters the Alcohol percentage is slightly lower, Mr Shields told me this is because the angels became too greedy. There are also two different bottlings of the new red stripe, one has a slightly higher alcohol percentage then the other. Unfortunatley i forgot the exact percentages,I believe it is 57,3 and 55,7 but I am not sure. sorry about that.
Secondly, The red stripe is much darker then the previous Green stripe,
third, They taste different. The red stripe has a slight sherry note and is generally less phenolic then the old green stripe. The new bottlings are way more accessible for the bigg audience where the old Green stripe was a peat monster with phenol spraying aromas you couldnt lose over a night. In my opinion (and lets be clear about this, it couldnt matter less since the green stripe is gone) the old bottling was superiour in every aspect, More then that it was a unique expression of Islay, one I couldnt compare with any Islays we have today. Whereas the Red stripe is much more mild and "just" another peaty malt on Cask Strength.
Yes, it won the whisky of the year 2005, i know and couldnt care less either. I believe Lawrence has both, unfortunatly i dont but perhaps Lawrence can do a HTH and state his findings.
If you can find a Green stripe anywhere, my advice: Get it!