I recommend Cleaner 5 http://www.discreet.com/products/cleaner/ , you'll be able to output to any format (.wmv, .rm. .mov, and all the mpeg's). You get an incredible amount of control over all your setting as well.

You can use .mov or .avi (and others) to import into Flash using the native Spark (Sorenson) encoding inside of Flash - but for higher quality and more control over bandwidth settings and the advantage of 2 pass VBR settings you'll want to buy either Spark Pro (Sorenson MX) http://www.sorenson.com or Flix Pro http://www.wildform.com (they both support stitching).

I find the best results using Cleaner to .mov - then using Sorenson Squeeze Pro or Flix to create my .swf's and .flv's.

5G