Linux has a pretty good video and audio converter called FFmpeg. FFmpeg can also convert from any sample rate to any other, and resize video on the fly with a high quality polyphase filter. However it is a command line tool and therefore it might be difficult for someone to remember all the parameters he can use. Here comes WinFF, a cross platform utility (it runs both in Linux and Windows). WinFF is a batch Graphical User Interface (GUI) that allows you to use FFmpeg to convert any video type.
WinFF supports mpeg, mpg, avi, mov, wmv and even flv as input formats. The default output supported formats are 3gp, 3g2, flv, h264, dvd, vcd, mov, wmv, divx, xvid and wmv. It also supports conversion for ipod devices and regarding audio it can mp3, wav, amr and m4a.
So install WinFF through your distributions Package Management System and run it. Click on the 'Add' button (1) and select as many videos as you like. Next choose one of the available conversion presets (2) and the output folder (3). Just Hit convert and the conversion will start! Simple, isn't it?
When the conversion completes you can find the converted videos in the output folder.
If you click on the Options button you will access some extra configuration options. Here you can adjust the Video Bit and Frame Rate, the video size, the Aspect Ratio as well as the Audio Bit and Sample Rate. You can also choose a 2 pass encoding for better results.
If you are familiar with ffmpeg or in case you want to search it further you can adjust the default presets. Click Edit -> Presets. Here in the 'Preset Command Line Parameters' you can change any settings you don't like. The official ffmpeg documentation is useful to learn more about ffmpeg options. You can read it here.
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