Server Based Movie Joiner?

There is a program called Transcode which should be able to do it. Check out http://freshmeat.net/projects/transcode/

As i know transcode not work with wmv/asf video formats.

I thought it did.. its been a year or two since i've played with the program though... time to install and check it out..

I'm Fairly sure MPlayer supports it although i'm whether you can split/join the wmv stream.. time to play with some of programs

It depends. WMV files are normally MPEG4 files with various
proprietary Microsoft headers and such thrown in to try to confuse
any software that hasn't paid the bribe to Microsoft to get the code
to get through their crap to the actual MPEG data.
WMV is no standard - there's no telling what Microsoft's software
might put into a particular WMV.
mpgtx, the Linux tool that is used to split, join, and otherwise manipulate
video, does handle the mpeg format that is hidden within a wmv
and can sometimes find the mpeg data in a wmv, but sometimes it can't.

Are you using the DRM headers that WMV allows on those videos?
If you aren't using DRM, there's no reason to have the
proprietary Microsoft headers and you can just use straight MPEG.
Then any of the standard tools like mpgtx can split, join, or
other manipulate the video and any of your customers can
watch the videos on any platform, rather than having to
use MIcrosoft Media Player on Windows.