PLUGINS
Plugins are very good ways to protect from hackers.  Plugins can protect from most hacks such as flying, speed hacks, and jump hacks.  When hackers join protected servers alot of them leave besides the pvp hackers.  This is the best way to protect against hackers in my oppinion.  
FAVORITE PLUGIN: http://dev.bukkit.org/bukkit-plugins/nocheatplus/
TIP 2
Dont give them warnings
Hackers join servers that allow them to admit to them hacking and get unbanned.  When hackers get this chance they obviuosly get to test how strict staff is with hacking.  The hackers will get to the right settings to not get banned.  Dont give warnings.  If the hackers want an unban make them donate to show truely that they wont hack again.  On my old server I had banned at least 10 hackers a day.  When I stopped allowing warnings or giving chances to get unbanned I may have had banned 2 hackers a day.

IP Ban if you own a cracked server
I used to be cracked and had played on cracked servers.  The server would only ban the name.  This is bad because cracked servers allow any name which means Hackers can keep joining with different names.  Many hackers are not that smart when they get ip banned.  This means it will take the hacker away.  Of course hackers can use a vpn but very rarely do they.

If this helped you please give me something SHINY!!!  It would really help me.