Your preferences/configuration from ST2 is in Packages/User (find it with Preferences -> Browse Packages). You can just copy that folder to to Packages folder in ST3.
Install the Python3 version of Package Control. Copy the Sublime Text 3 code for Package Control, open Sublime's Console (Ctrl `), and paste the code into the console.
Open your user's Packages directory for both Sublime Text versions from the menus using Preferences > Browser Packages... in Sublime Text. (Sublime Text > Preferences > Browser Packages... on OSX.)
In the ST2 Packages directory, copy all directories except these two: Default and Package Control. Paste all those directories into the ST3 Packages directory.
Restart Sublime Text 3.
(Optional.) Move your terminal / command prompt aliases to ST3.
Windows: Edit autoexec.bat in your user directory. Change doskey subl="C:\Program Files\Sublime Text 2\sublime_text.exe" $* to doskey subl="C:\Program Files\Sublime Text 3\sublime_text.exe" $*. Save autoexec.bat and restart your command line interface.
OSX: Remove the old alias by executing sudo rm /bin/subl in the terminal. Add a new alias with sudo ln -s "/Applications/Sublime Text.app/Contents/SharedSupport/bin/subl" /bin/subl.
(Optional) Enter your license key into ST3. From the menus, choose Help > Enter License and paste in your license key.
Aditional info for windows users, to make ST3 as the default editor after migration.
If you keep both versions or if you uninstall ST2... probably you will notice that you can't open files or associate open with by default with ST3.
I think I can help you get Open With/default editor working.
The problem is that the Sublime Text uninstaller doesn't remove a particular registry entry referring to Sublime Text 2's sublime_text.exe, which prevents Windows from adding an entry for Sublime Text 3's sublime_text.exe.
To correct it manually, open regedit and navigate to:
Computer\HKEY_CLASSES_ROOT\Applications\
find the sublime_text.exe entry, and delete it. You should now be able to set Sublime Text 3 as the default editor for anything you want.