Punctuation

Should you use an apostrophe s or just an apostrophe with a noun that ends with an s (for example, Jesus' or Jesus's)? Or what is the proper way to refer to a biblical verse: Rom 1.16 or Rom 1:16? 

Numbers

When do you spell out a number or not?

Terminology

Often specialized disciplines have many terms that are perhaps spelled a certain way or have a specialized meaning (for example, what's the difference between lowercase gospel and capitalized Gospel?).

Transliterations

Characters in languages that do not use a Latin script (e.g., Hebrew, Arabic, Greek, etc.) are given standard Latin characters for consistent representation where a word processor does not use non-Latin characters.

These general issues are discussed at length in §4 and §5 (pages 12-67) of SBLHS.