Transcoding few files at once or transcoding schedule

Hi,
Because, after many tests i'm sure that AMD Turion in my microserver is too slow to transcode some big .mkv's without shuttering while watching, without waiting few minutes AND my Sony Bravia KDL-42W705B isn't that smart to run those files without transcoding - is there any chance to transcode some files before time when i decide to watch them?
I mean, i have for example folder with few mkv's - if I want to watch them all in some short time, could I do something to transcode them and keep those files for later?
I could do it manually with ffmpeg but i don't think so that ffmpeg would transcode more then one file without separate command for every mkv i want to transcode.
Because, after many tests i'm sure that AMD Turion in my microserver is too slow to transcode some big .mkv's without shuttering while watching, without waiting few minutes AND my Sony Bravia KDL-42W705B isn't that smart to run those files without transcoding - is there any chance to transcode some files before time when i decide to watch them?
I mean, i have for example folder with few mkv's - if I want to watch them all in some short time, could I do something to transcode them and keep those files for later?
I could do it manually with ffmpeg but i don't think so that ffmpeg would transcode more then one file without separate command for every mkv i want to transcode.