Honestly? Leaving PowerPoint out of the mix would be the best thing here.

I'd probably convert to Flash.

If you're using PPT 2002 or 2003 and Windows XP or 2000 SP3 (but not Vista),
you might look into Producer, though. It's free and designed for this type
of thing.
http://www.microsoft.com/downloads/details.aspx?familyid=1B3C76D5-FC75-4F99-94BC
-784919468E73&displaylang=en

You might consider using PFCMedia or PFCPro and it's "Media From URL"
feature.  In a nut shell it allows you to place a linked video file from
within your presentation and the media file can reside on your server.

http://www.pfcmedia.com

Austin Myers
MS PowerPoint MVP Team

Provider of PFCMedia, PFCPro, PFCExpress
http://www.pfcmedia.com

To share a PowerPoint on the wepage, you have these options.
1. Put a link on a webpage for your vistors to download
Upload your powerpoint file to web.
Put a link on a webpage to the powerpoint file.

This option is easy to do but may cause some inconveniences for the
vistors.
Since you have video, you have to include the video and the
powerpsoint file in a folder to avoid broken links.
That means, visitors will have to download this floder in ZIP/RAR
package.
Of course, they will have powerpoint or powerpoint viewers to play the
file.

2, Save powerpoint as a html webpage
PowerPoint has a native feature to save a prentation as a html
webpage.
PowerPoint ->Save As-> Web page

This is good for a text-based presentation. If you have a lot
animations, transtions or other, the file may not played correctly in
the webbrowser.

3. Convert PowerPoint to Flash
If you can convert powerpoint to flash,  then you can insert this
flash to a webpage.
Actually, you can retain animiations, transitions and embeded video in
the converted flash.

How to convert PowerPoint to flash
http://www.ppt-to-dvd.com/forum/viewtopic.php?t=2141