I have used the DeLogo 1.3.2 VirtualDUB filter many a time to remove logos from my AVI that were captured off TV. It removes them fine but from a constant area for the whole movie.
To use this or other VD plugins, just copy the *.vdf file in the VirtualDUB/Plugins folder. Same for VirtualDUBMod. To use them, in the Filters option in Video, click Add and select the plugin you want. Then follow the directions for each different pluggin. The plugins normally have Readme.txt files or similar that explains how to use them. You then need to Save AVI using DivX or Xvid as the compressor and set at the same (or a tad higher) bitrate as the original.