I've been trying to find the best choice myself.
In the end I believe Hamana was the one which felt the most interesting. It gives easy access to changing folders back and forth, has previews so you can quickly look for the chapter you want, and offer many other fun adjustments.
I also have built my own viewer for practicing my Japanese. It opens two comics so you have a raw and a scanlation open, then it flips pages on both at the same time so you always have the raw and translation available for reading. On top of that it also allows zoom (though only to 100% of source size) and cross-zoom (so that you can see the raw in zoomed in ontop of the translation).
I'm quite happy with my program, but it only supports folders and zips, been trying to figure out how to handle rars.