If you want cross-platform compatibility, .flv would have to be your first choice. Flash has now surpassed even Java in reach. Adobe claims that 97% of desktop users have Flash installed.
I really don't think there is another choice. There are some players for various formats written in Java. But the load time for the applets puts off users.
Next after that is WMV, and that's where you are now..
The choice of codec, though, is difficult right now. .flv is a container format - it can contain content encoded with different codecs. And this will be an ongoing issue with Flash, as they seem to support one more latest greatest gotta-have codec with each release. You need to make sure to look at the statistics for % of users with each version of Flash installed. Flash 8 and 9 is far from universally-installed at this point.
Sorensen Spark (based on H.263) is available in Flash 6-9.
On2 True Motion VP6 is available in Flash 8-9, and is much superior.
I believe Adobe has announced they will be supporting a codec based on H.264 in the future. Apparently this is supported in recent beta releases.
I would go with Spark for now, and be prepared to support the new H.264 codec in the future. Or you could provide both Spark and VP6, and plan to add the new codec later. Given the superior characteristics of H.264 along with it's projected future popularity, you might just skip over VP6. I don't think VP6 is going to get much uptake with publishers, with H.264 announced.
If you go with .flv, there are a number of royalty-free and commercial player applets available. The Wikipedia Page on "Flash Video" lists quite a few of them.
Now do you see why I want you to "use the source"? You're probably going to re-encoding those 200 videos several times in the future. I don't expect the forward march of codecs to stop.
You'd put yourself in an ironic position converting from one highly-compressed lossy web-oriented format to another is that you are going to wind up doing it several times - copy of a copy of a copy of a copy.
The irony is that each codec is better than the previous one, but your video quality is going to degrade with each conversion.
Which brings us to:
I'd say use the best edited format you have and convert from there. And hopefully you choose a good edited format. High-end editors generally have a proprietary format that is as close to lossless as possible while being practical about disk space.
It's not *quite* true that you won't have degradation in a conversion as long as the input format is higher quality than the output format. For this to be true, the input format really has to be quite a bit better than the output format. And there are many factors related to specific codec characteristics.
For example, any format that uses P frames is really unsuitable for editing. Yes, consumers edit MPEG. I suppose it's fine for movies of your kids and dog. A good editor will at least give you the option to not use P frames (use only I frames, which stand alone) in the MPEG output. (P frames are frames present in the input that DO NOT EXIST in the output. The player has to predict the content of these frames based on nearby frames. )