The version at Costco is the CD/Download version of TurboTax and is a bit different in functionality and pricing (though TurboTax doesn't control retailer pricing at stores like Costco). The main pricing difference is that version includes a state preparation, but it does not include a state e-file. You have to pay an additional charge to e-file your state (except in NY), but you can paper file your state for free.
Briefly, the main differences are the online program gives you the flexibility to work online, so you can access your returns through multiple formats (online, mobile device, tablet) and your work will be stored online. The desktop program is local only, which means you must install the program and you can only work on that computer. Your returns are also only stored on your computer, so you would be responsible for making sure you keep backup copies etc. The advantage the desktop program has is, since you have already paid up front, it includes a Forms Mode - where you can view the forms behind your tax return as you are preparing it. The desktop version also allows you to do multiple returns (up to 5 federal e-files) using one program.
Overall, the desktop program has more functionality, but the online program has more convenience. If you only have one return to do, the pricing generally works out to be similar in the end (unless you don't mind paper filing your state). But, if you have multiple returns to do (i.e parent doing returns for children), then the desktop can be more price advantageous.
