If you wish to find the main source of all the plugins, feel free to look here: http://dev.bukkit.org/server-mods/

Now for personal suggestions. Overall, this is a rather picky issue, I would personally use these if you are just starting out:

For beginners:
Essentials
bPermissions
AntiCheat
WorldEdit
WorldGuard (Requires WorldEdit)

You can swap out Essentials with CommandBook if you want a better but not as common experience.
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As far as the "best" plugins, there are many different types, of which you can't exactly distinguish as "best". But I will give the lists of some basic ones, and describe them as best I can briefly.

Permissions plugins:
bPermissions - Easiest for new users
TotalPermissions - A new permissions plugin being developed by Lord_Ralex and myself.
Privileges- Simplistic and fastest permissions plugin. Not as popular, but a recommend
PermissionsBukkit - Has some hooks with things like McMyAdmin
GroupManager - Has some pre-made configs, but I personally dislike this.
PermissionsEx - Most versatile, most buggy and easily breaks

Overall Commands:
Essentials - the most used, simplest to handle
CommandBook - much more lightweight alternative
AdminCMD - a newly made one, has a few nice features
jCommands - not the biggest or well known, but is under dev and holds the most basic needs

Block Logging:
LogBlock - I personally use it now. It is simple and gets the job done.
Hawkeye - Another popular choice, has a couple extra kicks.
SWatchDog - One of the few logging plugins made with Tekkit in mind.
CoreProtect - Another rarity, this plugin can log blocks without the use of MySQL. However, using MySQL is a benefit in the first place, so I would not recommend using it. It is great if you are a smaller server however.

Anti-Cheating or Anti-Hacking:
Nocheat - Evanprime's original anticheating plugin, now discontinued. (Link removed, as most things bypass it now).
NoCheat+ - An up-to-date continuation of the original NoCheat
AntiCheat- An under development plugin by the essentials team.

Anti-Spam:

STAB - Also registers multiple IPs
SpamGuard - Another popular choice, protects against various things like CAPS, repeated messages/commands, and gives warnings.

Global Banning Systems:

##Note:
Many global banning systems are very disliked by people, due to the fact of a repeated history where server owners will either ban due to previous bans, or not allow players to join because of it. This is not the way I personally recommend you use the tool. In all honesty, you should be using these plugins as a reference, and as a banning tool. You should never judge a person's level of punishment based on a previous ban, but rather on what they have done specifically to you. So with that said, onto the plugins...

McBans - The most popular by far, has the largest database.
McBouncer - A nice McBans alternative, with a good web gui.
Glizer - Second most popular. Not nearly as many rumors/shortcomings from this as McBans.
MineBans - Smaller banlist,

All of these can be referenced at once via this Lookup tool, or by the Fishbans checker plugin.

Anti-Xray:
Xray-Informer - Works in correlation with Logblock, queries your data tables to find mining ratios.
Orebfuscator - One of the most rigorous methods, masks the ore from clients. However, it will be resource intensive unless properly tweaked.