My wife and I finally stopped procrastinating and bought our Christmas gifts. We thought about buying via Amazon but ended up just making a trip to Toy's R Us. One key reason was that we were worried the items wouldn't get to us in time if we bought them online. Of course that problem could have been avoided if we hadn't procrastinated. 
I figured we probably paid a bit more for the convenience but I figured it was worth it in this case. However I wasn't sure how the prices would compare exactly. To find that out I decided to do a small pseudo random sample of toys and compare the prices on Amazon and Toys R Us. I decided why not compare to Walmart too. The toys I picked were kind of randomly selected but picked based on what I thought would represent a different set of popular toys for kids of different ages and interests. Amazon :
Call of Duty Black Ops for PS3
= $54.96LEGO Ultimate Building Set - 405 Pieces (6166)
= $27.99 Barbie I Can Be A Cheerleader 2 Pack Doll Set - Barbie & Teresa
= $42.99 Justin Bieber Justin Bieber Concert Kit 31050
= $29.99 (pre-order)Toys R' US :
Call of Duty Black Ops for PS3 = $59.99
LEGO Ultimate Building Set - 405 Pieces (6166) = $31.99 (out of stock)
Barbie I Can Be A Cheerleader 2 Pack Doll Set - Barbie & Teresa = $21.99
Justin Bieber Concert Kit = $16.99
Wal-mart
Call of Duty Black Ops for PS3 = $54.54
LEGO Ultimate Building Set - 405 Pieces (6166) = $29.97
Barbie I Can Be A Cheerleader 2 Pack Doll Set - Barbie & Teresa = not available
Justin Bieber Justin Bieber Concert Kit = $17.99 (pre-order)
The results are pretty mixed. The Call of Duty and Lego items are a bit cheaper at Amazon and Walmart than Toys R Us. The Barbie set and Justin Bieber items are cheapest at Toys R Us and way overpriced at Amazon. The Barbie item isn't even available at Walmart. I suspect the Barbie item is an older item that is now obsolete. Looks like the Justin Bieber item is new and may not be shipping yet but Toys R Us seems to have it. For both of the high priced items on Amazon they are being sold by 3rd parties rather than directly from Amazon.
Totals all 4 items : Amazon = $155.93, Toys R Us = $130.96
Totals for 3 available items: Amazon = $112.94, Toys R Us = $108.97, Walmart = $102.50
Who's the winner?
Overall Toy's R Us wins since they have all four items for the cheapest price but they lose because the Lego set is currently out of stock. Walmart wins on the 3 items they have but they are a loser since they don't have one item at all. Amazon since all the items are available but they lose since they are the most expensive any way you cut it. I see no clear winner here. Each has pros and cons. In the end I'd probably go with a combination getting the video game and Legos off Amazon and the Barbie and Bieber items from Toys R Us.
Of course this is just a random sample of 4 items and really doesn't prove anything. If I picked 1000 items I might find that the 2 high priced items on Amazon are a fluke. But this does at least demonstrate that you can't make a blind assumption that one retailer is cheaper than another in general.
Shipping
I did not count up shipping costs. Amazon shipping is generally free if you buy $25 or more, but there are exceptions. Walmart will generally ship items to your local store for pick up for free. Toys R Us shipping is more expensive so they lose on that one but they have many local stores where you can get the items without paying shipping.
Sales Taxes
I also didn't figure sales tax since those very in every state. Amazon often wins on this one as they are an online merchant and you not charged sales tax usually (with the exception of Kansas, Kentucky, New York, North Dakota, or Washington). If you buy locally at a retail Walmart or Toys R Us you'll pay local taxes. The sales tax issue really depends on your state and how its charged.
Bottom Line: I don't see a clear cut winner. It depends on the items you buy and how shipping and sales tax works out for you. Be careful with some 3rd party items on Amazon.