Sadly, you'll still miss some of the nicer sides of packages. First, you obviously won't get automatic updates for it. Second, if you are thinking that when doing a clean install you can just print the list of your apt-based packages and get the same ones when installing the new system, forget it. The list will contain not only the actual manually installed packages, but also all dependencies set to manual, so you cannot just take a look of all installed software. I found it best to make such a list manually in gedit. Third, you'll still have to take care of dependencies, just it will happen at the time of making the package instead of the time of compiling manually. The same goes for things like a main menu item. So in some cases, the added complexity of making a package just isn't worth it.
On the other hand, if the eclipse authors haven't provided a way to uninstall your built-from-source eclipse, it is a very good idea to make a package first so apt can remove it for you later. Also, if you will be installing it on more than one PC, a package will be very handy.
There is a tool which will create a package for you, but I've read that it isn't very good with resolving dependencies. Never tried it myself, but if you want to give it a try, here's the link: CheckInstall