To summarize...
As in iOS, you can organize your Launchpad icons as you please using drag-and-drop. You can reorder apps, move them from one page to another, and even put them in iOS-like folders. Note that Launchpad folders are entirely independent from the /Applications hierarchy: creating a folder in Launchpad won't create a folder in /Applications, for example.
Your problem seems to be related to the fact that you've got so many apps. Again like iOS, there seems to be a maximum on the number of pages of apps Launchpad can handle. If you really need all 400+ apps on your Launchpad, there's not much you can do other than reorganize everything into folders to free up some slots. But I doubt you need instant access to everything Adobe has ever installed on your computer, so you have a few more options to clean out your Launchpad:
- Delete apps entirely. There's probably a few apps on your computer that are just sitting there, never to be used; you can free up space on your Launchpad and on your hard drive by getting rid of them.
- Apps from the App Store can be uninstalled directly from Launchpad by holding option/alt and clicking on the black X over the app's icon.
- Any app can be deleted by dragging it from the Finder to the Trash.
- Alternately, you can use something like AppZapper to delete an app along with any hidden auxiliary files.
- Move apps out of Launchpad's sight. Launchpad looks for apps in /Applications, /Developer, and ~/Applications. If you like those folders to be as pristine as your Launchpad, you can move your extraneous applications to a different folder. Launchpad will lose track of them as of the next reboot.
- Just remove the Launchpad icons. Finally, Andreas Ganske has developed a preference pane which modifies the Launchpad database to show or hide whatever applications you want.
If you just want a clean Launchpad, option three is probably your best and easiest answer. Options one and two are there if you like to keep your /Applications folder clean, too: useless apps might as well be deleted, and your CS4 uninstallers could probably be moved somewhere a little more out of the way until you need them.
Finally, you hint at having problems with having Launchpad duplicates. As I mentioned in an answer to this question, this may be a problem of actually having more than one copy of the same app installed.
Hope this helps clear up some of your upgrade troubles!
I had the same issue initially. After upgrading to the latest version of Parallels (which also solved the virtualization issue), all Windows applications were moved to ~/Applications (Parallels) at the first start of Parallels and the icons now don't show up in Launchpad any longer.
Best Answer
It seems that apps that the only apps that are directly removable from Launchpad have to be installed through the App Store.
For every other app, you can simply do it the old fashioned way:
Many people are using folders to reduce clutter of apps shown in Launchpad. (while eagerly awaiting either an update or some tools to manage Launchpad layouts.)