I'd usually suggest that you post this request in the Japan forum- however, part of your question is more general, so it might be best served here after all.

Personally, I'd rather have a stop-over enroute, but October is still rainy season in parts of South East Asia (I'm thinking the Andaman coast, i.e. Phuket) although the beaches just South of Bangkok might have good weather. You'll find your money will go a lot further if you can do this (Thailand, Vietnam etc are considerably cheaper than Japan/Okinawa). There are lots of Low Cost airlines that serve Singapore, Malaysia and Thailand, so you should have a lot of choices on where to go beyond where the official stoppover airports are.

As for Japan in October - this question has been asked a few times, here's an example from someone else for October(http://www.flyertalk.com/forum/showthread.php?t=326292). However, if you are going at the BEGINNING of October, I strongly suggest you register at www.CEATEC.com for a taste of the future that goes way beyond anything you'll encounter at Akihabara (and it's free!). It takes place a little to the East of Tokyo in a state of the Art conference centre - Makuhari Messe. Info: click here but the dates and links are different for 2006.

If you plan to be in Kyoto on the 22nd October, be aware that there is the Jidai Matsuri (a festival) on on this day - click here for info - if you want to go, RESERVE YOUR ACCOMMODATION IMMEDIATELY! It disappears extremely quickly.

Do be sure to check out this Master Thread:
http://www.flyertalk.com/forum/showthread.php?t=530019
with quick links to some of the Japan Forum's 'greatest hits'.

Despite the occasional typhoon, October is my favourite time to visit Japan.
My tip is to make sure your itinerary isn't too tight and has a degree of flexibility as a typhoon can disrupt the train timetables (this and earthquakes are the only things that do!).