You could try this tool based on LibWiiSharp. It's a modification of the base TPL converter example that can operate on a TPL that contains multiple images. It helped me when I recolored Marta's hair in DotNW. Zip has source plus binary.
http://www.mediafire.com/download/5ukv25ebkdamr0m/libWiiSharpTPLConv.zipThe TPL to Image tab will show you all the textures that are inside the TPL (scroll through with the Texture dropdown). It will let you pull them out as various image types (I usually choose PNG, you could use any lossless format, so don't use JPG). It will also tell you about the individual textures as well, such as their size, Format, and Palette. This info is needed when re-packing the TPL.
On Image to TPL, it's less intuitive. I suggest ignoring the Convert button - it works, but it can be confusing. Instead, favor the Add button. The number in parentheses beside the Add button is the index in the TPL where the new input image will go; so Add (1) means that the input image will be the first texture in the TPL; in other words, the TPL has zero textures.
Every time the output TPL file is changed, Add (n) will update to reflect where the input image will go. This allows you to not just replace, but add images to a TPL. Load a TPL with 4 images, it will say Add (5), select an Input Image and click Add and it will now say Add (6) and your TPL will be automatically saved with the new fifth texture added to it.
Oh yeah. With all of this, make sure you have a few extra copies of your images. Do all of your work on this application with copies and keep the originals somewhere safe. There aren't a whole lot of safety checks or confirmations in this app.
When you select an input file, it will try to guess what a good output file will be. If this output file already exists, you will be appending to it, not over-writing it. So delete this output file (you are working on copies, right?) or give it a different name. While the Input Image textbox only shows one file, behind the scenes the textbox's tag will keep track of multiple files that were selected. So you could select all four PNGs at once and make them into a TPL.
If you do this, make sure you click the LAST FILE FIRST, and then hold shift and click the FIRST FILE LAST. In the Open File Dialog it should then list the files in the correct order (1,2,3,4); if you do this wrong and click the first file first, it will look like (4,1,2,3) instead, so cancel and try again.
After you select your input images, and output TPL file name, set the Format and Palette to match the original (which you got off the TPL to Image tab, right?). Then IGNORE the Convert button, and
instead click Add (1) (if the output TPL has no textures in it). It will automatically create/append to the Output TPL file, and Add (n) will reflect where the next Input Image would go (so if you add 4 PNGs to a TPL, it will say Add (1) before and Add (5) after you click the Add button).
If you want to "clear" any setting, you should just quit and re-open the file. Make sure to delete any previously existing output files if your intent is to create a new TPL, because this tool always adds images to an existing output file.
EDIT:
Any time you create a TPL, load that TPL back into the TPL to Image tab and make sure that the textures look right. Be careful not to hit Convert on the TPL to Image tab or you could overwrite your Input Images (which wouldn't be so bad because you're working on copies, right?)
EDIT2:
@megazig, you mentioned "Zetsubou"? I googled, can't find any source or binaries, the github is dead. It also says it can't handle CI formats. The LibWiiSharp converter example I posted to mediafire can handle CI.