Seems like there's been some activity on this issue lately.
I just finished some testing on trunk (r2178). I tried TGA and PNG, lossless and not, transparency in the image and not, using GridImageUpload.exe. The results were good. All of the images were faithful reproductions with and without alpha.
The only problem is that a 24-bit TGA is still getting an alpha channel added, even though it doesn't have one to begin with. This doesn't affect the way that the image looks at all, but it causes the SL viewer to treat it like a transparent image. For example, if you put the texture on two intersecting prims and move the camera around, you will see the textures fighting for which one should be on top. PNG doesn't seem to have this problem. A non-alpha PNG stays non-alpha when it is uploaded.
So, overall, I'd say that this is a big improvement. If we can eliminate the superfluous alpha layer on 24-bit TGAs, then I think it's perfect. For testing, you can use the plywood.tga that I uploaded previously.
Note: I'm having some unrelated issues with trunk which I reported on the mailing list. Having some problems with prim rezzing. I only mention it to let people know that trunk might not be completely stable ATM.