I usually try to get them in small paper bags (nice paper bags with handles) with paper (tissue type) on top. This seems to go over well. Similar to Ashikaga's post above.
Of course wrapping is nice as well, but is not required if it looks nice and exotic. Just don't hand over something in a plastic bag, remember the nice/exotic part.
My girlfriend tends to get the bags from the store while buying and repackage later. So they look nice, but also has the store name on the bag. It's the image, especially if the store is not something available in Japan.
Of course as a foreigner, just giving omiyage is good. People in Japan expect, but don't completely expect from foreigners, so (my personal belief) you make points for giving, no matter if it is perfect or not. You don't lose out by trying.
In addition, little things work well, especially food items that can be shared. Local candies, etc. from your country that can only be acquired there. I like giving food type items because a family or office will tend to all share and try what you give. That way everybody gets something and you don't have to get everybody something. (it would be hard to pack all the stuff to come otherwise)
Good luck