Here's my profile for the project 64 emulator. This uses default controls. Includes emulator shortcuts in the command set & has a default config. Other than that, nothing special. You'll probably want to use the built in support for analog control. Also, I realise that project 64 has great built in support with one exception, it doesn't separate the Z axis for the triggers (when using MS drivers). Which would give you problems in games when you need to use the left & right triggers simultaneously.
EDIT: Cool... Here's a nifty little trick some people may not know. I remember playing GOLDENEYE 007 on the 64. It had a setup option that would allow a player to use 2 64 controllers (one in each hand) to play with analog control for movement/look. That was kinda weird & I'm not sure if other games had this.. but project 64 will allow you setup a single controller as player 1 & player 2 simultaneously. So you could play certain games ( I'm not mentioning any roms here ) with your 360 controller & have analog control on both sticks. Now that is pretty damn cool!