For all those in the process of upgrading to 2013, I thought I'd offer a few tips and tricks that I've picked up. Hopefully they make your life a little easier.
First, you'll need to download and copy the attached files to the locations called out in the ReadMe.txt file (just substitute 2013 for 2012 wherever necessary). This will install an addin to your Revit 2013 program called File Upgrader. There are instructions within the readme on how to use it, but it essentially opens and saves every .rvt, .rte and .rfa in the folder you specify as a 2013 file. Bonus: it also copies the directory structure (folders and subfolders), so you can maintain your directory structure from release to release.
Key point: It will not update .rft (family template) files. So you have to rename the files with the .rfa extension, then run the File Upgrader, then rename the files as .rft. This is also how you can make changes to the family templates; while they're named with .rfa extensions, they're editable, so add all the categories, linetypes, notes, etc. you want.
Double bonus: to batch rename file extensions in Windows, Shift-right click on the folder that contains all the .rft files, and select "Open Command Window Here". In the command window that opens, type "REN *.RFT *.RFA" (without the quotes) and hit enter. You'll have to do this for each subdirectory. Then, when you're done upgrading the files, just do the same thing and rename the file extension back to .rft.
I've found this tool to be a much better batch upgrade utility than the one that comes packaged with the Revit install, but your mileage may vary. Also, kudos to Saikat Bhattacharya of the Autodesk Developer Technical Services team, who originally developed this addin.