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aPerf and Opis are very useful (Forge) profiling tools. aPerf also has a lot of useful preventative features such as spawn rules and strict item grouping.
PowerNBT is a very handy Bukkit plugin too, which doesn't quality as non-MCPC+. Its most useful purpose is the in-game editing of offline player data such as inventories.
MCEdit is probably the most useful non-MCPC+ tool, as you will need it when you have to remove crash-causing machines from your map. It is also 100% compatible with Forge data.