I was going to use cherry pie filling but my friend said she thinks, and based on some reviews, that the pie filling is too liquidy, ruins the cake and makes the liners soggy. I was going to drain the liquid or maybe cook it with some cornstarch to thicken it. Either that or just go by a sleeve of premade filling. 
I always use jams and preserves. I buy some locally from an Amish lady, and I also like to make my own sometimes. Cherry preserves can be harder to find than other flavors, but this brand is sometimes available at grocery stores http://www.amazon.com/dp/B000EXWL8C/?tag=cakecentral-20
You could also check for cherry preserves at Whole Foods and other health food stores as well as any gourmet type stores you have in your area.
hth
Are you talking about filling the cupcakes before baking or after? Of course I've never tried pie filling, but I don't see how it's any different than using the sleeved fillings...they're pretty much the same consistency. That's why I don't understand your comment about ruining the liners or making the cake too soggy unless you bake with them.
I baked Nutella inside vanilla cupcakes and it did get messy. I've used Henry and Henry raspberry filling and a jarred lemon curd for fillings, but they've all been inserted after I baked and they worked great!
I think the cherry pie filling will work. On my runnier fillings, I don't make the hole as deep to help with structure. You can make the hole a little wider and mound a little on top. I would just try it. I read somewhere that the cherry pie filling is easier to eat if the cherries are chopped coarsely.
Thanks everyone for your replies. I still have the pie filling but bought sleeved cherry filling instead. I keep hearing conflicting things. . someone says bake the filling in the cupcake and some say after. . .they have a long ride on Sunday. . . . oh dear. . .
You should try one or two cupcakes and leave them for a few hours to see how they behave.
How long is the ride on Sunday?
If the hole is not that deep, the cherry pie filling might be OK. I don't know how you're making the hole, but here's this tutorial using an apple corer, just don't go too deep. Most plungers and other methods might make too big a hole.
http://www.flickr.com/photos/mka900/3445619960/
In general, cupcakes are filled after baking....think of baking a cake first, then adding filling and icing, right? Your sleeved filling will work fine! Bake and cool the cupcakes then fill by using an apple corer, knife, or spoon to scoop out a small hole in the cupcake. Then add the filling with a pastry bag or spoon. You can swirl your icing right on top of the filled well. Here's another way to do it:
http://bakingbites.com/2007/09/how-to-make-filled-cupcakes-step-by-step/
The ride is over an hour on Sunday. I have 2 in the oven now, one filled and one not filled. I think they'd taste better filled after, too, get more flavor from them but filling as I scoop the batter would save time. . . .I'll see how they come out. I wish I had experimented sooner, I still have 60 cupcakes and a double 8" to make and have to make the icing and all of that. I can't find my apple corer and could not find one in the store so I was going to use my melon baller. . .maybe the cone shape might be better, though. Thank you so much! 
I use sleeved fillings and haven't tried anything else, but I wouldn't mind expanding my horizons! I have a Wilton (I think it's Wilton, anyway) tip for filling cupcakes. It's like a regular cone-shaped tip with about a 2" tube on the end. I insert the tube into the baked cupcake and squirt filling into it. It works like a charm! The only problem is that you can't use fillings with anything chunky in them, but I'd probably whirl the cherry pie filling in the blender and use it with this tip anyway. Lemon curd, huh? Mmmm!
I saw someone make the hole with the end of a wooden spoon. For your experiment... put thm in the freezer like Cupcake Wars and you can fill them sooner. I always make two cupcakes with a new recipe just to decide how high to fill the liners.
You can always put them in a cooler for the trip. Refrigerate them ahead of time. Use that fake ice in little bags and they will still be cool. Take them out 30 minues before serving.
Scp I just emailed my friend and was waiting to hear from her when you answered first, I was thinking that, too, feeze them so they don't fall apart. They are made with cake flour and are very soft. They are for my neighbor, I think she has a cooler and I was ask her if she has ice packs.
Thanks you guys are great!!
I most often use sleeve fillingin a pastry bag with either a Bismarck Round Decorating Tip 230, you just stick it into your baked and cooled cupcake and squeeze until the filling just starts to rise out of the cuppy or I use any of the smaller round tips, same thing with the baked cupcake, but I will poke it in - in three places to make sure there is a good amount of filling. Ice the top and done. Super quick and easy. I only do the core and fill method if it's a chunky filling like apple and I don't bake my fillings in the cupcakes ever. Good Luck!
HI all... Would LOVE to get your input ~
Making cupcakes & want to fill it with Paula deen's "Not yo Mama's Banana pudding"... The Deen recipe has a cookie layer with a fresh banana then topped with the pudding~ DELISH!
I know for the cupcakes I should fill them with the pudding mix after baking BUT my question is How do I add a piece of fresh banana?
I am planning on baking the cupcake with a Nilla wafer on bottom - should I place a piece of banana on top of the cookie before I add the batter to bake? OR should i place a little piece of banana in the "cored" center of the baked cupcake before sqeezing in the pudding??
Due to the decoration on top - rubber ducky baby shower theme - I can not just place a slice of banana as a garnish.
My searches have mostly led me to Banana cake cupcake - not what I'm looking for. I'd really appreciate your input - 1st time doing a stuffed cupcake! :0)
If you put the banana in before you bake the cupcakes, the banana will bake, too, and the results will probably not be what you're looking for. I like your idea of putting a piece of banana in the hole where you're going to squeeze the filling. That way you'll get the REAL effect of banana pudding.
I think the banana idea sounds very intriguing. It sounds delish. My fear would be the banana turning a disgusting brown or softening too much in the cupcake. Wonder if the pudding would keep it fresh? And you'd almost have to keep them cold wouldn't you?
Oooo, what if you baked a banana cupcake and filled it with just the pudding? (Don't mind me...I'm just thinking!)
I make a strawberry filling that works really well with my vanilla bean cupcakes.
I just puree strawberries, then add the strawberries with sugar, and some almond extract, and a tiny bit of cornstarch to a pan and mix those over medium/high heat until they get thick(usually about 15 minutes)
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