Here are the highlights.
This is based on my experience with only two EMs of similar vintage, Bally Bon Voyage (BV) and Bally Monte Carlo (MC), so it is far from complete. Just my own ideas and opinions.
I would always start by saying there is nothing wrong with the ideas that EMs should never have leds in them. There are some people that find it ok to use leds as well. The good thing is, it is pretty much easily reversible. Save the old incandescent and they all go back in fairly easily.
Next, from what I have seen and from what I have read, and also based on lots of discussions I had with Art at Comet, it seems that every EM machine is going to be different as far as what is the best solution. There is so much variation that what works with one may not work for another.
Finally, you have to factor in that different people have different tastes. What looks good to one looks hideous to another.
I break it down to 4 separate parts.
1. Playfield GI. These are the only bulbs where you can actually see the bulbs themselves, thus the trickiest. Generally it seems best to get a look as close to the incandescents as possible. The best start are single led, warm, and clear tops. The Comet retro ones come somewhat close it appearance, brightness and color(warmth). But in the end, you have to accept that the leds will never look exactly like the incandescents. It's just not gonna happen, they are two different technologies. So if you can't stand "close" you could decide to leave the GI as incandescents and try leds on the rest.
Frosted or natural white will give a whole different look to the playfield. It might look horrible, it might look ok, it might look great. You have to try it and see. It will depend on the color scheme and artwork.
2. Playfield Inserts. The brighter 2 led versions in white seem to look good but again some experimentation will show what looks best. Frosted will help prevent a highlight ring from showing through. But now you can have the flickering or ghosting problem, which shows up as the machine is played. Various things like pop bumpers being hit or other targets can cause them to briefly light. On BV you can just barely see it, you might not even notice it. On MC it is extremely obvious and pretty annoying. So now here you have to use non ghosting versions or add the resistor.
3. Backglass GI. Frosted warms seem to work fine. I can't see any difference in what they call "spotting" between those and incandescent. The bulbs are bright spots behind the back either way. If you used frosted it should have about the same amount of diffused spread. The retro warm clear might look better in the score reels because you can actually almost see those. One thing to deal with though are any that are blinking. BV has several of those. The incandescent versions versions are analog so it is totally random as far as the blink rate, thus giving the cool random blinking effect behind the logo. The led blinkers are fixed rate. You can get slow and fast blinking leds and mix them up and it looks ok. Or just leave an old style or two in there to keep the randomness.
4. Backglass Funtion Lights. These probably will have the same flickering/ghosting problem as the playfield inserts so non ghosting or resistor mods are needed. Frosted seems to work well behind the backglass for player up, ball in play, tilt, game over, etc.
All of this doesn't even take into account color leds or possible mods.
As far as color leds on the backglass, it might look good in some spots or maybe not. You have to try and see. Even though there seem to be good opportunities for color on the MC backglass, nothing I tried there looked any good, so they stayed all white. But BV had a few spots where I thought some blue and pink looked good. This is in the realm of personal taste.
Pic of BV backglass here with all leds and some colored.
http://www.xsvtoys.net/images/pinball/bon%20voyage/Bon%20Voyage%20backglass%202.jpg
As far as color leds on the playfield GI, I think that needs more exploration. It will definitively vary by machine. It will depend on the color scheme and the overall look. I tried some on BV and nothing looked good. It looks best with all white. The MC is more open to possible color. It has a lot of,green background and a white red and blue color scheme with poker chips. I matched it all with color leds and it looks kinda ok. But I don't think I would leave it that way. But that doesn't mean another EM might not look nice with some color on the GI.
As far as led mods, such as extra lighting behind the flippers or in certain areas of the playfield, that is wide open. I noticed some EMs are pretty dark. Maybe they might look better with more lighting? This needs more experimentation.