I was told we could use boxers - you can put the tail through the hole, but you'll need to remove for potty breaks.

I ended up not using anything -  I had purchased boxers just in case, but returned them. 

Maybe it would be helpful to get your wife involved in Tripawds.com.  Once she sees how well adjusted the dogs are and how supportive the group is, maybe she can begin to accept that this is a GOOD thing for Boomer.

I know this is really late since the original post was in 2010, but I have used opaque panty hose.  Cut them off wherever you need them to cover on the leg or hip and cut off the side you don't need.   Works like a charm when you put a surgical bandage on top of the stitches or wound.  I also use boys or mens stretch boxer shorts on my standard poodle.  

I would also appreciate suggestions for covering up a rear leg canine amputation site - not for cosmetic reasons but to protect it.

The doctor said not to try to bandage it tightly - just let it be open.  But, Ginger likes to sit outside most of the day, and I don't want flies or other bugs getting into her incision.  She sits on clean blankets to protect her from the dirt, but that doesn't protect her from bugs.

I also want to prevent her from licking it at night (without using the clinic collar/cone) when we're not watching her.

We tried putting shorts on her, but when she slid her butt around on the floor after a few time, she had pulled them down so the elastic was sitting on the incision which probably isn't good.