alexh -> can you give me an example of a game, that causes screen to flicker? Maybe I do not fully understand your problem... Is this a problem that occurs also in WinUAE?
I've got both 100Hz 29'' LG TV and 7-years old polish 21'' TV and I didn't noticed any problems - using RGB connection (RGB/EuroSCART) and PAL50 modes, but no flicker-filter.
About "Agnus setting" - try changing "Video chipset" setting from "Agnus" to "AGA" and see what you get.
BTW, I've tested LAN NetPlay in WinUAEX (2 Xboxes + System Link) Connection few days ago. It works with some problems (any little glitch will cause game to desync completly, although we were able to play Sierra Soccer for 5 minutes - impressive
) but I doubt that it would be usable over Internet (due to pings, etc.).