Here's what I've done for my two girls, one born in 2009, and one expected to arrive this November:
For 2009: 2009 U.S. Silver Proof Set, 2009 American Silver Eagle (bullion version), 2009 Lincoln Commemorative Silver Dollar (proof and uncirculated), 2009 Uncirculated Mint Set, and one 2009 Australian Lunar 1-oz Silver Proof Coin (celebrating the Year of the Rabbit).
For 2012, very similar: 2012 U.S. Silver Proof Set, 2012 American Silver Eagle (bullion version), 2012 Star-Spangled Banner Commemorative Silver Dollar (proof and uncirculated), 2012 Uncirculated Mint Set, one 2012 Australian Lunar 1-oz Silver Proof Coin (celebrating the Year of the Dragon), and one each of the circulation quality 2012 S-mint-marked quarters (as they come out).
Doing all of that gets a little pricey (runs over $300 for each kiddo), but I think it provides a pretty cool selection of the year's coins representing proof, uncirculated, and bullion, and all of the mint marks.
I'll likely leave the uncirculated coins in their packaging and put them away, but for the proof coins and
ASE for each daughter I hope to leave the proof set coins in their lenses, put the other coins in air-tites, and have the coins custom-framed together, along with a baby picture and a matte with the name and date of birth.
I'll admit that including commemoratives is a little weird, and I only did so because the 2009 Lincoln and 2012 SSB commemoratives are the only ones I find appealing and own in my own collection, and probably would not have put a commem in either girl's birth year set otherwise.
I'll also admit that the Australian Lunar Coin is something that most wouldn't do, but I did so because my wife is Vietnamese-American, and the Lunar calendar is part the Viet culture. Many foreign mints are doing the Lunar coins (I think Canada started in 2010), but I picked Australia as I liked their designs the most, even though I'm not a fan of a living monarch being depicted on the obverses of these coins.
Hopefully we've given you good ideas on what you can do for your little girl. Good luck!