I just started to write out a list of all the LE and CE's I know of, when I remembered that Defcon has pretty much most of them already listed on his site!
Here's the link you need:
http://www.defconsoft.co.uk/special-editions/
One I believe he is missing from his database is the Grand Theft Auto: Limited Edition, which comes with a soundtrack CD and features a different cover design (Gold, grey, purple) opposed to the usual design
Not to be confused with the later released GTA Limited Edition which is a compilation of all three PlayStation GTA games
I also own another GTA LE (Sealed) which is the Platinum version of GTA plus London 1969 packaged together side by side. However, I have reason to believe that this was just a retailer bundle and not an actual legit LE package