Yes, with shoes.
I've been rocking a pair of no name low-tops for about 6 years, and they're about spent. So I go to a store (Kohls) and buy a pair of Tony Hawk skate shoes. Not because I'm a skater, but they looked close to what I was wearing and what I liked. They ended up hurting the top of my right foot. So I exchanged them for the next size up, from 10.5 to 11. Still hurts, especially the tendon that runs on top down to the big toe.
What the hell?
I've got several theories as to why this hurts. Only the right foot hurts. Maybe that foot is just sore or injured and new shoes put a spotlight on it. I've got hairy feet. ever mash a tight winter hat on? After you take it off, your scalp hurts. Could this be the same thing? The tongues on these shoes are enormous. And are held in at the top by a thick band of elastic. Too much pressure? Are skate shoes built that different?
Strangest issue is that this pain is only on the top of the right foot. The left feels great.
I'm out of ideas. I don't want to keep wearing them to fully break them in, only to have them still hurt. Then there is no way to return them. I've never had this problem before.
You know, I thought that. But why would it screw with just one foot? Repeatedly?
You'll need to keep the laces loose on skate shoes. I'm not a skater but I think the elastic allows the sole to stay in contact with the grip-tape on the board while doing aerial tricks. Is the tag rubbing? Are there any fibers poking out?
It could be because it's a store brand (Tony Hawk apparel is only sold at Kohl's). I've worn a bunch of skate shoes from DC, Etnies, etc. and even a store brand called NSS, and haven't had a problem with rubbing.
I've worn Airwalks, Vans, and Etnies. I've never experienced what you describe.
I wouldn't call it rubbing. More like discomfort from a constant pressure. Like if someone pushed down on your shoulder with their thumb. Doesn't hurt right away, but have them hold it there long enough, and it'll start to ache.
Appleseed, I hate to say it..but it sure sounds like something may be wrong with your right foot. Unless you got a mis-matched pair or something (the odds are pretty set against getting two mis-matched pairs in a row, though). Any "small" accidents lately? Missed a step on a staircase/rolled over while climbing down under a car/insect bite while barefoot?
And I gotta admit, I don't know how old you are..most of the stuff I mentioned didn't bother me when I was 30, but now that I'm sneaking up on 50, seems it takes for-berkeleying-ever for even a little tweak to heal. 
Put the end of a broom stick handle inside the shoe with the tip touching the top inside. Pull the shoe around the tip stretching the material slightly.
Try it on.
Do it again.
Try it on.
Repeat
as
necessary.

I had this same problem with a hiking boot. It eventually went away, but it took a lot of breaking in.
Have you looked inside the shoe? Perhaps a black widow spider has taken up residence there.
I had the same problem with a pair of Timberland hiking boots. The tendon on the top of my right foot, that big one. I wore them around the house for weeks trying to get them to "break in" by then the store wouldnt take them back. I tried streatching them, and wearing the laces loose. eventually I took them to Goodwill.
Never had the problem before nor after with any other shoe. I still havent tried another pair of Timberlands.
Lesley
SuperDork
11/4/10 8:56 a.m.
Isn't that weird... I had the same experience with Timberland hiking boots.
You going formal or casual? Like a little heel, or no? Are you looking to project fun, sexy, practical, what? Do you need to be able to wear them with lots of different outfits? I'd recommend you try maybe a little lower cut because the top of your foot's hurting, but the hairy-foot thing might not work well with that.
Ok, although typing this makes me realize most of the advice from women's-shoe-land can't help you here, there is one tip that doesn't cross the gender divide often enough: Take your shoes to a good shoe repair place. Preferably one who also does orthotics. Have them check out the fit while they're on, then professionally stretch them for you. You'll have to leave them a couple days to get them properly stretched, since a quick stretch is pretty useless (the leather rebounds).
One last thing: It's your right foot because it's probably bigger, since most people's dominant foot (and hand) is the right one, and your dominant one is bigger. (And because of this, mere stretching might not be enough. You might be one of those folks who needs to buy 2 different sizes of shoes.)
Margie
Well, right now, I'm wearing the old beat down no-names. No discomfort at all.
I'm going to try on some shoes this weekend. I tried that idea earlier, but after my foot was already hurting. Sucked. Gonna go early in the day and see how it feels then.