Mike, if you need to rencode video, just use xilisofts video converter. You can do hundreds to thousands of conversions at once.
http://www.xilisoft.com/video-converter.html
Works on both PC and Mac. You can dump (as far as I know) as many videos as you need and do a batch conversion from just about 1 format to another.
You'll have to do a specific output and wait (however long it takes from your thousands of videos) then make a new list of settings.
Pro Media: $6000
Sorenson: $600
Xilisoft Ultimate (All the tools): $59.95 and it'll do the job you need it to do.
Others are suggesting cloud services or offering you to ship it to them. All these options are just not practical.
Cloud: unless you have a home uplink of 50/100 mbps (even then) it's not practical. Those videos probably run hundreds of gigabytes
Shipping product: Not very practical and would probably take weeks or months on the size you have.
Good luck with your choice.