We need to convert bunch of swf files to youtube compatible format/flv. Anyone knows free or not expensive command-line tools which can help to do this.

Any advice will be highly appreciated!

From flash CS4:

Note: you can only convert flv which have no action script.

Step 1: Open your source file in flash (.fla)

Step 2: File > Export > Export Movie (export as .mov)

Step 3: Close the file and Create a new file

Step 4: File > Import > Import Video > Launch Media Encoder (Button)

Step 5: Add all the .mov into the queue and start the conversion

http://www.zamzar.com/ is a free service that delivers your converted file to your email straight away and has many conversion file formats.