I have some gifs (1000), that i want to make transparent. What i want is the old trick f treating the upper left pixel of the gif as transparent when doing the conversion. Any command line and/or batch processing to do this?

I use the full installer version of XnView which comes with NConvert, both are freeware. XnView/NConvert has a batch convert process in Tools->Batch Convert. Another freeware image view with batch conversion is IrfanView. Now rather either programs can set the transparency exactly as you are wanting is unknown to me, however it's worth a try.