For what it's worth about being accepted, I have interviewed at 2 airlines (successfully), and had my computerized logbook reviewed by the UK CAA as part of getting credit for my FAA certificates toward a CAA/JAA ATPL.
My electronic logbook was accepted with no problem and no question at all of these interviews and reviews. I recommend you take the time to do it. It definitely was time consuming transferring 13000+ hours into the computerized logbook, but now it looks so much neater, plus I can set any filter imaginable to run a total of my flight times.
Which logbook you use is just a matter of personal preference. I use AeroLog Pro with its Pocket PC companion. It does a good job for me, but I hear good things about Logbook Pro and Flight Level, also. They all give you a certain free trial period to see what you think about them.