Amiga emulation can be a little tricky, as there were a number of different models of Amiga, and many of them were somewhat incompatible with each other. Most games were programmed for an Amiga 500, which used a 68000 processor and the OCS chipset... however, later games were meant for the Amiga 1200, which used a newer, faster 68020 processor and the AGA chipset which offered some enhanced video modes (Many games were released in two different versions, since the 500 was still quite popular even in the dying days of the Amiga). WinUAE will let you set up a ton of different hardware configurations, so you'll have to see what works best for the games you want to play.
As for games, check Hall of Light's Top 99 page: http://hol.abime.net/top99.php
Some of my personal recommendations would be: Alien Breed, Superfrog, Gods, Scorched Tanks, Ultima V, Pools of Darkness, Turrican 2, Moonstone, Pinball Fantasies, Xenon 2, Awesome, The Chaos Engine, Dungeon Master, Chaos Strikes Back, Neuromancer, Oil Imperium, James Pond 2: Robocod, Liberation: Captive II, Nuclear War, Frontier: Elite II, and Project X.