It really depends on why you're doing this. Is it for a member friend? If so, is there any certain message you're trying to get across? If that's the case, then hop over to the topical guide and look through the scriptures on that topic. Just make sure you check the scriptures first, because some of them aren't really all that relevant. Oh, and it wouldn't hurt to read what the Bible Dictionary might have on that topic. There are often extra--and more powerful--scriptures listed.
If not, and you're just trying to highlight key scriptures, then I'd go with the ones from either Preach My Gospel or the seminary lists (you can probably find both online, though the ones from seminary are often the same ones from PMG anyway). Those are the ones that come up the most often.
If it's for a non-member...well, when I prepared BOM's for people on my mission, I always highlighted the ones that meant the most to me: the first three paragraphs in the Introduction, the fourth paragraph, and the last two paragraphs. Also Moroni 10:5 and the parts of 3 Nephi 11 where Christ appears. Those are the most useful, and in the case of 3 Ne. 11, the most beautiful parts of the BOM.
The color you use doesn't really matter. It doesn't hurt to use something bright that will stand out--pink usually works--but make sure that the words are still clearly visible (red isn't often a good choice unless you're using a pencil and not a marker or highlighter). If you're highlighting more than one topic, though, I'd use a different color for each topic.
Oh, and I find that crayon pencils (or just crayons) are really great for this. They don't bleed through, at least. You can find a pack for about two bucks at Wal-Mart...which is good, because I often ended up giving mine away while I was in the field. After an investigator's child shoves them up her nose, the urge for giving gifts becomes almost unbearable.