For those in the Philadelphia area, where can I find good preserve fillings for thumbprint cookies?

Green Aisle Grocer on East Passyunk & Gray's ferry.. amazing flavors all handmade & locally sourced.

The baking section of most grocery stores stock Solo Fillings that come in all those flavors you've mentioned.

If you're in the Rittenhouse area, Di Brunos is a solid option, as commenters have mentioned. Whole Foods works too. And then, there's also the farmers market on Saturday mornings, where there is sometimes a stand that sells preserves.

Have checked Wegmans (they gave me blank stares) and Whole Foods knew what I wanted but doesn't carry it. I'm located in Cherry Hill, NJ. I'll definitely check out Di Bruno & RT Market.

What exact town/county are you in? I own a home in Bucks County, and can steer you if that area is within striking distance.

Reading Terminal and DiBruno Bros would be my first two stops. There's lots of farmers markets in the area too, at least some of which will have vendors with what you're looking for. Eat This had a stall at my farmers market (now closed for the season) and they have great preserves; they're in Erwinna, about 30min north of Doylestown, and participate in markets all over the area. I've also had Two Sisters Canning, again from my farmers market; they're a relatively new business, but their products definitely have that small-batch taste.

I would check Di Bruno brothers, just off Rittenhouse Square. They have a pretty extensive offering of unusual gourmet spreads, etc.

Wegman's or Whole Foods would probably have prune and apricot, not sure about poppyseed

You might try a Pennsylvania Dutch (Amish) market. I haven't gotten there yet, but there are several stalls at the Reading Terminal Market - supposed to be very good. Bell's Market also does eastern European products - went there once for Hungarian paprikas, but I'd bet they have those too - poppy seed and prune especially are used in many pastries from that area.