It is more down to personal taste. I'm a newbie with LEDs, and Greg (RTBB) has been a fantastic help in LEDding three games - ToM, Terminator 3 and Tales from the crypt. The resto threads cover the LEDs with results.
I think the first thing to go is decide if the game can be improved with the use of LEDs. The three examples above were INCREDIBLY improved with LEDs. But a game I restored in between ToM and Terminator 3, WCS 94, did not look good with LEDS. That's my personal opinion. As the salesman at JB Hi Fi once told me - "I'll put tape over the manufacturer's name on each of the Televisions in the store, and the chances are you might pick a no name brand over a Panasonic. Everyone has a different set of eyes.." That's the analogy I draw.
Once you have decided that the game should have LEDs, you need a wide selection of LEDs at hand. Start with the inserts. A later game like ToM uses super brights. We used standard 180s, but they didn't look right. Ghosting was not a problem on this title. I tried using super brights on T3, and the playfield was littered with ghosting LEDs. I reverted back to 180s and it looked much better. Make sure you play the game, as ghosting can be a real problem once things get hectic. Ghosting is not a huge problem in attract mode.
As mike suggests, use the color of the insert as a guide. Be aware that a blue insert on a Stern won't be the same as a Bally Williams or Data East. This is where you need a wide selection of LEDs for trial and error. I don't use white LEDs in colored inserts.
GI - Use 180's and fit the plastics as you move around the playfield. Note that light is dispersed and can create awesome effects - bleeding and blending in with surrounding hardware.
Backbox - Use 180's and play around with colors. This is where you may have to use the standard globes in some places. The difference LEDs make to a backbox is profound.
Flashes - 89 and 906. Look AWESOME on and under the playfield. Not so good in Backbox
PO bumpers - Use the specific LEDs. They look great
I ended up buying a mixture of 100 or so LEDs from RTBB. Mix and match as you go along. Be prepared to experiment. It is great fun !
Hope that helps..