Since 2005 I've used primarily AF 30B transformers (S gauge layout), a spike protector by Scott's Odds 'n Ends (no longer available, but still working great) and 7A fast-blow fuses -- one per block and every siding. Together they have provided and continue to offer solid protection. However, if I were to do it over today I'd use PSX-AC units by DCC Specialities. We have them on our club layout and they are fantastic. Definitely very fast-acting (critical attribute) and resettable.
PS Their RRampmeter is also very good, especially if you run DCC, which I do in addition to Legacy and conventional.