For combining videos use:
cat video1 video2 > video3
Click here for more info.
If you would like to use the combined video in website, you could try a new technology, called popcorn.js. You should see this video to understand how to combine multiple videos without any software and to start any video from wanted seconds. It's very interesting.
For the whole process of cutting and combining videos maybe you need a script like this:
avconv -ss 00:01:00 -t 00:02:00 -i $input -c:v libx264 -crf 23 $out1
avconv -ss 00:08:00 -t 00:10:00 -i $input -c:v libx264 -crf 23 $out2
# add as many lines as you like
cat $out1 $out2 > $combine
You only have to change the names of variables at the start of the script.
Also You could try MENCODER for joining videos:
mencoder -oac copy -ovc copy -idx -o output.avi video1.avi video2.avi video3.avi