It happens to me when I switch over to a new system/controller and my hands aren't using to using the differently shaped controller. I recall having hand pain when I started playing a lot of PSP after I'd been playing Wii or the DS exclusively. Usually that goes away withint a few days later.
I have tendonitis problems with both of my wrists, and I've had issues when using the Wii Remote/nunchuk in games that have a lot of waggle. When I first got the console, I quickly realized that I couldn't play for nearly as long as I could with a standard, modern gamepad. I can play with a GCN/Xbox 360 controller (without rumble) for hours without pain, but an hour or two with the Wii motion games, and my wrist will hurt. It's usually pretty mild, though. Thankfully, I don't have to worry about that anymore. 
I experienced something similar when I was playing GoldenEye 007, which is why I switched over to the classic controller pro.
Didn't have a problem since.
I think it does have something to do with the Wii-mote and how it's shaped.
Also, I did have hand cramps when I played Bayonetta and other games. It was because of the intensity of the game and all that button smashing. I don't have problems with FPSs or RPGs though.
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Now Playing: Golden Sun Dark Dawn, God of War Ghost of Sparta, and DKC Returns
The Wii ain't so comfortable, particularly when you hold it horizontal NES style. PSP is also poor, and I've had problems with my thumb knuckles getting sore with prolonged play of the DS.
Only time my hands feel pain is when I get back into a session of Guitar Hero or when I go on a two day gaming binge (like 10+hours a day for two days). I tend to grip real hard on things (like steering wheels etc)... so it's my own fault.
No problems with wrists or anything like that.
Most of the Wii games I play just require relaxed and tiny wrist motions, as I don't tend to buy waggle stuff outside Wii Sports & Resort, so most of the motion is just pointer use with the occasional flick of either the remote or the nunchuck. Then again, I never had issues with those games or Red Steel 2 either, and the only game that actually made me tired was the rented Force Unleashed with its stupid waggle-for-every-action mechanics, so, I dunno... Still, they shaped it like a TV remote to make it look familiar but it should have probably been a bit more ergonomic even if its appearance ended up a bit weirder. On the other hand, that could negatively affect its usability in NES mode, which would be bad. I never had pains from any controller though, the biggest issue I've had is with the PSP making some of the (surprisingly) unused fingers numb with prolonged use, the way it's held. But maybe my wrists are used to strain from all the mouse gaming (not that anyone would call that waggle either).
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The wii-remote would have to be one of the least painful controllers I've used, with the potato pad and even the smaller xbox controller easily being the most painful.
I also haven't really had any trouble with swinging and what have you being tiring of painfu; except I haven't been able to play Red Steel 2 lately lol. Other than that it's been plain sailing with the Wii.
Wii-remote sideways could be almost as bad as the potato pad, but luckily nothing has required me to do that for long periods of time. Other M. 
The potato pad.
Same as Foolz the worst pads for my hands seem to be the xbox ones. they just don't seem ergonomically sound. my favourite is the gamecube controller (just talking about the feel of holding it). it just seems like it was made for my hands. dual shock is OK too, i got used to it a long time ago. The wiimote is annoying when having to play sideways but not painful or anything.
The only times a controller/control method caused me physical pain (at least this generation) has been sometimes on the psp (and i can never play that for very long anyway) and trying to play metroid hunters on DS was a real nightmare (i felt weird things happening to my hands so I thought best to give up)
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Listen to Wu-Tang and watch Kung-Fu
Ah yes, the gamecube controller was really comfortable. The dual shock is probalby my favourite controller because I'm so used to it. Can be painful sometimes, though.
Acutally, there's one thing that is almost as bad as the potato pad. The GBA: SP. :X
Had no problems with the DS phat so far, though.
I don't think this is a wii problem as I frequently get wrist pains and it's the typing on the keyboard that is the problem. I use wii a lot, probably a lot more than you Dvader as I buy more third party games, but it's never given me a problem for several years now.
The only controllers that have given me problems is the huge burger sized Xbox controller where I had to strain my normal sized hands to reach everything. And actually the gamecube pad, but only for one game - Harvest Moon a Wonderful Life.
That game was so great, yet they insisted that you water your crops individually, twice a day
My wrists felt like I was a real life farmer.
Using Wii IR FPS games can give you a wrist pain, but its only a problem when you don't play in the right position and don't support yourself properly. Sonic Colours has no IR so it shouldn't be causing any strain.
It's a problem you have when you first start playing IR FPS, most of us had it way back in 2006. Eventually you learn what is comfortable for you and that should negate any problems you have. You should never be holding the remote out in mid air for long periods of time without your wrist or elbow supported either by your leg or a cushion.
gamingeek said:Using Wii IR FPS games can give you a wrist pain . . .
Dual-analogue, FTW! 
Ravenprose said:Dual-analogue, FTW!
Someone has brainwashed you like in Black Ops.
It has nothing to do with my wrist, its my joints at the knuckles usually. After some time I will realize that I have been clenching the wiimote and nunchuck in a grip for so long that when I relax my hand I feel a tiny bit of pain. I dont think we are meant to have clenched fists for hours on end, with a controller the hand is open, with a wii its clenched.
I had numbness in my whole hand when fighting Dark Samus on Hyper difficulty in Prime 3. I then realized that I was really clenching my wii-mote really tightly. Once I relaxed the numbness was gone. Don't clench it too tightly and you should be fine.
Iga_Bobovic said:I had numbness in my whole hand when fighting Dark Samus on Hyper difficulty in Prime 3. I then realized that I was really clenching my wii-mote really tightly. Once I relaxed the numbness was gone. Don't clench it too tightly and you should be fine.
But that is my problem, I am subconsciously holding the wiimote, when I am into a game I am into a game. There are moments when I think about my hands and I realize they have a death grip on the wiimote and nunchuck. When I am aware I try to stretch out my hands in loading screens or down times. There is no other way to hold a wiimote and nunchuck, your hand has to be wrapped around it.
I have no idea why you have the remote in a death grip. Are you afraid of it flying loose and smashing your TV?
Use the strap
The strap is for babies and women. The wii-remote strap too.
I have been gaming for a long time and for the most part I never have pain in my hands after playing. That was until the Wii. For some reason the Wiimote gives me occasional hand pains. Its usually around the knuckles, its nothing bad, its just there. Maybe I am getting old and my hands will have horrible arthritis but I can't remember a time a controller did this to me.
I think its cause of the shape of the wiimote. Its something you grab, like a stick and you shake it around, much like masterbating, but I dont masterbate for hours on end. I think that kind of gripping of something for so long isn't good. With a controller your hand is shaped differently, your fingers are spread out, I think its less stressful on the hand.
This is just something I notice and it happened again right now after a Colors session. Am I the only one this happens to. This is not my hand getting tired, these are joint points or something.