I will address at least a few of your questions:
1) Re. Joystick Selection
U360's are wildly popular, and they really are the best (IMHO) do-it all joystick. To my knowledge there are no other joysticks out there that really do it all, or change profiles via software. You'll likely want the harder springs and some restrictor plates for them.
2) Re. U360 Configuration
U360 all the way. none of the others are done via software. The only complaint or difference by people seems to be that some people like physical restriction in controls, versus just the software changing. But the optional restrictor can help with that, if that bothers you. Personally, that doesn't really bother me though.
3) Re. Ultrimac I-PAC4 Configuration
I will let someone else confirm this. I know they can absolutely be reconfigured. The part I am questioning is whether the IPAC can handle mouse clicks. I was under the impression that a keyboard encoder would not be able to handle mouse clicks. But I usually use GGG's KeyWiz myself. Anyway, a lot of trackball options out there do come with mouse buttons, since a trackball is basically just a fancy mouse. So if the IPAC can't do mouse clicks, you should be able to find a trackball that can.
4) Re. LED Push Buttons & Encoder
You can have as much control as you want with a PAC LED, or a LED-WIZ if you use a piece of software such as LEDBlinky. You can control the brightness (intensity), you can flash them, light up only the controls that are necessary for the specific game you are playing etc. You can also put on a little light show when the game is paused. Look around, you will see lots of videos of this in action. Here is one from one of my arcades.
The lighting part is somewhere in the middle of the video.
Regarding the buttons, see my review I posted
here There is also paradise arcade, which you will see in the review, which offers a similar button alternative. I love all these buttons, especially since you can make your own inserts, or use
pongo's vinyl. Some people don't like how clicky (noisy) they are, but I don't find it to be a problem. As for the resistors, with each LED that each vendor provides, they all have built in resistors. So you don't need to add one yourself. Makes things a lot easier.
5) Re. Control Panel Overlay & Side Art
I've never printed my own graphics. I have always ordered from
GameOnGrafix. They use some kind of polycarbinate laminate thats pretty tough. They can also print on this polybanner stuff if you plan to put plexiglass over your CP. I've used both and personally, I like the normal polycarbinate laminate stuff they offer, with adhesive. I have used a plexiglass overlay, and its pretty cool, but not really necessary, especially if you get the polycarbinate laminate from GoG.
6) Re. Lighting – Cold Cathode, Neon Flexwire/EL Wire
I can't speak to the other stuff. Thus far I have only used a sound sensitive Cold Cathode light bar, which you can see in my above video. There was nothing to that, but again, I wasn't doing anything complex with it...
7) Re. Additional Emulators/Common Frontend
The part of the idea of a front end is to link up all these different emulators. So you will only need one front end, not multiple. You will have to configure or design menus for each system/emulator, but it's still all done through one program. There are a lot of front ends out there. If you are using a good, decent power PC, you could look at HyperSpin. Hyperspin offers you the ability to make a theme for each individual game (instead of just each emulator as a whole). Some people aren't into all the glitz of that (or arent using a powerful enough pc) so that one isn't an option for everyone. I also like MaLa. It's free, has very good support with a forum member who listens, and is pretty easy to configure. I used Maximus a while back, but you have to pay for it (did not confirm if this was still the case) and I'm not sure what state their development is in. Like I don't know if someone is regularly updating it or not. Might have to look into that. Theres also a few other front ends out there, but those are the major ones. It can vary wildly on opinions, so try them out, see which one you like.
Re. ROM movies/Sample Clips
I believe all front ends support movies/screen captures. EmuMovies is bar none the best supplier for these videos. Constant updates, constant improvements, just a great community too. You do have to pay to get other emulators besides MAME I believe. I am not personally aware of any other alternatives for videos besides EmuMovies. In my opinion, this is because EmuMovies does it so well, there is no need for an alternative. And no, emulators do not come with screenshots or videos. You have to get those yourself.
Whew! that was a lot of typing!
