Will try out Manga2Ereader later this week when I have little bit of time to experiment.
The problem I have with converting PDF's to Mobi is that you can no longer switch the page into Landscape mode, so If you haven't already split the page in the PDF you are stuck with the orientation that you use when creating the file, if it is just images.
And in some comic strips, you just want the sunday strip to be bigger, so can;t really be automate it.
Also, I have a Sony PRS-500, so PDF means that I only have to create one file for both

, something that means one less headache for me.