N64 emulation is notoriously bad, even today. It's a mess of plugins and while you can get the games playable and looking more or less how they used to, the accuracy is pretty far off. You are going to run into this problem with any of the 3d systems basically.
Also while you can emulate anything up to a n64/psx with a modest pc, PS2/Xbox/NGC emulation takes a rather beastly pc, so if you are going with a micro footprint, you can pretty much scratch those off the list.
Ok a few cents worth of advice:
If you are going to attempt some of the higher end systems you need to put a 64bit os on there. Most of your 3d console emulators have a 64bit version and you'll get better performance by as much as 40% on some of them.
There aren't any front-ends that I know of that are very console-specific. Also the emulators will fight you on that as well. Ideally you'd want to be able to do everything from the gamepad, but the emulators fight you on that. It's something I wanted to tackle myself, but it's in the queue behind 14 other projects.

Laptop or Micro PC you are going to run into the same issues if you choose to use the 3d emulators.... you need a really fast processor and a really powerful video card. Neither form factor is really known for these things, with the exception of maybe one of those crazy expensive gaming laptops.
There are remote control programs that allow you to use a remote to simulate key presses in windows. Simulated key presses won't work on anything that uses raw input though (mame, mess, some of the more oddball emulators, ect) so keep that in mind.