First, there are generally 3 color temperatures available--warm, sunlight, and natural/cool. With warm bulbs, the color looks a bit yellow. Sunlight is roughly neutral, and natural/cool is a bit blue. For most things, I generally go with sunlight.
I've been using comet bulbs for years--they've always worked well for me.
Typically, for GI, I use: 1smd sunlight frosted. Sometimes 2smd in darker areas.
For the backbox, I typically use natural/cool 1smd bulbs. Depending on the look of the backglass, sometimes I use frosted, sometimes I use no lens. Although, more often than not, I use frosted with translites, and no lens with real backglasses.
For inserts, I typically color match the red, blue, green, and purple inserts. I use sunlight bulbs for orange and white inserts. No lens on bulbs pointing directly at the insert, and for bulbs that are sideways, I either use flex head or frosted. For small inserts, I usually use 1smd. For larger inserts, I usually use 4smd or 2smd.
The only time I use warm leds is on EM games. The GI on EM games is also the only place where I might use clear lens blubs to try to replicate the look of incandescent bulbs. Otherwise, I stick to either frosted or no lens bulbs. With the clear lens, the tend to cast visible rings of lights on backglasses, inserts, and plastics.
The only time I use cool/natural is in the backbox, especially with yellowed translites, to help offset the yellowing.
I never color match plastics on the playfield or colors on the backglass. I think doing that just overpowers the existing colors of the game.
For flashers, I generally use the 5smd, 8smd flat, 8smd tower, and 8smd flex head. If a flasher is basically directly visible by a player, I'll use 5smd. If not, I'll generally use an 8smd flat or tower. Flat; I'll generally use if the bulb is basically being directed in a particular direction. Tower; if if the light is omni directional, like under a large colored dome. Flex; usually if the bulb is sideways, especially when there's a large insert in the center of pop bumpers. I generally don't color match flashers, and pretty much let the domes/plastics/inserts do the work. In special cases, I've used 10smd flashers, such as in the AFM mothership saucer.
That is generally my approach to adding LEDs to games.
: Also, I haven't used non-ghosting bulbs. Plus, it's less expensive to just stock one bulb type, and non-ghosting bulbs are generally more expensive than their standard counterparts. Most games don't actually need them, since there are workarounds for ghosting. For classic bally/stern, the siegecraft LED add-on boards work fine. For WPC, just use the LED ROM fix. For gottlieb system 3, the ghosting is so minor, it's barely noticeable.