I recently got a Kindle and I also have a small manga collection, so of course I tried to read some manga on my Kindle. The experience was pretty lousy, so I tried using Calibre to convert to MOBI or PDF first and Mangle to resize my images but found those solutions unsatisfying.
Ultimately I wrote my own frontend to ImageMagick to convert my manga scans to a Kindle suitable layout. I'm going to post some screenshots to see what people think. Soon I'll release the application as it still needs some polishing.
This is the startup screen which is just used to add and sort scans/pages.
This is the heart of the program where you define the page layout and image filtering. You can preview any changes before exporting. It might look confusing but most things are set to a sane default and you can always preview to see the impact.
This is the preview window which shows the preview in a device-screen sized area. Use the 4-way to pan across the image.
The main feature in my app that I don't think others have is 'Render Pan' which makes reading on the Kindle much easier for me. I like to read in landscape mode and it makes using nudge shortcut difficult. (When it works at all.) Using render pan produces an image like the following such that when you pan a screen's width or height you get the appearance of a only moving a smaller amount. Since the sections overlap, you never end up with a word bubble half on one screen and half on the next. Imagine reading by seeing the red then green then blue highlighted section. You'd get the illusion of panning in 3 even amounts down the image.
I don't really know if this is the best site or forum to annouce my app. I'm not really a forum guy and don't know anywhere better. Let me know if you have any thoughts and I'll try to release something you can play with soon.