I almost never use the clutch to shift up, there's a pretty wide rpm range where it will just naturally shift, and if you do it towards the lower end of that range there's almost no change in accelleration, doesn't feel like you're putting any kind of stress on the transmission.
For downshifting I'm usually slowing towards a stop and then I use the clutch to jump down to netural. If I'm downshifting one gear for more power, I usually don't use the clutch, if you do it just right it seems like you get a pretty ideal amount of power coming into the more powerful gear, feels like it was designed that way.
I've never had any transmission problems.