For the record I *ONLY* ever used fully supported hadware with amithlon boxes. To not do so hurts more than gfx performance (vesa modes eat into cpu resources, its quite horrible). A c2d@3ghz-ish *IS* required for a flawless aga experience under 68k uae on amithlon. You can get away a lot less using only 68000/ocs/ecs software, but its not a case of perception,... you absolutely need the 3ghz c2d to have a flawless aga experience.
One word of warning though, ne careful who you listen to when it comes to amithlon,... lot of people who dont even understand it o know it seem to offer advice, which is mostly wrong. A Voodoo3 is for example a terrible choice. It's simply not supported properly. Anything Nvidia up to gf5xxx (although gf5xxxx is iffy, safer bet to use a gf4ti or gf3 based card, or a matro g100,g200,g400,g450,g550 card. The Matrox cards are also the only cards that support multiple monitors off one card in Amithlon as well.
As for Winuae vs Amithlon, theyre different beasts, but typically the heavier the load, the more Amithlon shines. In heavy situations amithlon can be up to 2x as fast. Winuae needs to do many, many more reads and writes due to lack of direct hardware access. This is only with 68k too, the fact amithlon can run x86 native amiga software is another bonus (there's an x86 native uae for amithlon out there too somewhere which is obviously somewhat faster than the 68k version). The more involved the software being run, the more Winuae can suffer in comparison.