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What software would you recommend?
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Technically, all Linux GUI Software for CD burning uses the same command line tools in the background. So you should simply use the GUI tool you like most - the technical results will always be the same.
I personally prefer K3B for everyday work, it's quite easy to use.
If you want to to more fine tuning, you might have a look at xcdroast.
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Does it matter If I backup files from ext3 partitioned drive and a fat32 drive onto the same CD session?
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No, as long as Linux can read the source file system it doesn't matter.
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What filesystem is the most common/should be used so the backup CD can be read from Windows and Linux? Or don't I have to worry about this?
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CD-ROMs all have the ISO9660 file system (special cases and historic hardware excluded), readable on both Linux and Windows. No reason to worry ;-)
Regards
ric.