I have two of all iWork '08 apps, two of all the apps in the utilities folder and various other things. When i search for them in the finder there's only one of anything i have duplicates for in launchpad 
Here's what happened to me:
When I installed Lion I noticed duplicated apps too, then I realised, whatever I had inside a folder in the applications folder was now duplicated in the root folder (apps folder). This seemed to be a problem in Launchpad, which listed the app two times.
This is very true. I don't want to have to take all the apps in folders out, especially the utilities folder just to clean up the launchpad >_>
This is how it looks for me. I have a utilities folder and then all the utilities out of a folder.
Image