The field of Mac OS X system maintenance and tweaking utilities is getting crowded. There are, of course, MacJanitor, the venerable freeware and Cocktail, which also started out as freeware (now $12 demoware) has developed a following, and version 3.x has been rewritten from scratch.
Cocktail also established a basic interface and feature set motif for this sort of utility, a variation of which is available in Koingo Software's $10 Mac Pilot and the freeware OnyX utility, too. However, there are also now the very interesting freeware DoktorKleanor, the $7.95 shareware Panther Cache Cleaner 2.1, and the $7.95 shareware TinkerTool System, and - not sure that's all yet, but those are the ones I've checked out so far. My Mac is currently very well maintained!
If you're running OS X, you really ought to have at least one of these programs and use it regularly in order to keep the big cat happy and optimized. They all work fine in my experience on my 700 MHz iBook running OS X 10.2.6. Which one(s) you choose will depend on your personal taste and whatever secondary features tickle your fancy. They are all either shareware or freeware and relatively small downloads, so you will probably want to check out several of them. - Tip Jar
Cocktail is a general purpose utility for Mac OS X 10.2 or later. The application simplifies the use of advanced Unix functions, gives access to hidden Mac OS X settings, and lets you easily optimize your system.
It is a smooth, powerful, and simple to use utility with all major features arranged in five basic categories and a "Pilot" that lets you maintain your system with one click of the button.

Cocktail 3.1 includes new features for locking or unlocking files and folder, improved disk spin down time feature, and new settings for choosing startup language, setting window resize speed for Cocoa applications, and showing or hiding Exposé blob.
Cocktail started out as freeware and gradually morphed through donationware to $10 shareware and most recently $12 shareware. It's a nice little application that works extremely well, and you can still check it out for free.
Version 3.1 is available as a free update for all registered users.
Disks
System
Files
Network
Interface
Pilot
New in this version:
System requirements: Mac OS X 10.2 or higher with the BSD subsystem installed
Cocktail is $12 shareware.
Koingo Software's $9.95 Mac Pilot shareware utility enables and changes hidden features in Mac OS X and related applications as well as performing OS X system maintenance tasks like updating prebinding, removing log files, repairing permissions, running cron scripts, deleting caches (including swapfiles), and more.

Comparisons to products like Cocktail, TinkerTool, Onyx, and others are inevitable. In terms of user interface, Mac Pilot most closely resembles Cocktail and does some of the same things. It is $2 cheaper.
MacPilot also adds the ability to control hidden features in Mail, Safari, and Address Book, such as enabling Java and JavaScript, and control of animated images.
Safari
Dock
Finder
System
Logs
Miscellaneous
Happily, most of the categories offer buttons to "Revert To Defaults."
The latest Mac Pilot version 1.0.2 adds:
System requirements: Mac OS X (has been tested on Panther)
So far, Mac Pilot is a nice little Jack of many trades application and well worth a look. It is 15-day $9.99 demoware.
OnyX is another OS X utility offering maintenance, optimization, and personalization for Mac OS X. Like Cocktail and Mac Pilot, OnyX also makes it possible to configure certain hidden parameters of the Finder, Dock, Safari - to remove a certain number of files and repertories become cumbersome, preview the different logs and CrashReporter and more, and it's still freeware.

Onyx utilizes the increasingly ubiquitous Apple brushed metal appearance theme, to which I am not partial, but this is about as stylish a rendition of it as I've encountered. Very snazzy and professional for a freeware app.
The Onyx interface displays eight tabbed panels:
OnyX is Freeware, and works with all Macintosh computers running Mac OS X version 10.2.x or later (with subsystem BSD).
New in version 1.3.0:
New in version 1.2.9:
There is also an excellent and comprehensive OnyX Help manual included explaining in detail every OnyX function - one of the best I've encountered in any software, and certainly the best among these utilities.
While there are distinctions and some differences in features and function, for the most part OnyX seems to be pretty much equivalent to Cocktail and Mac Pilot for most users' purposes. Since the latter two are shareware and small downloads, you can try all three easily and decide which you prefer.
Another freeware OS X disk maintenance utility that also adds a bunch of troubleshooting features in addition to the basic housekeeping routines is the new DoktorKleanor.

DoktorKleanor installs in either of two modes:
This mode automatically launches a series of tasks which fix the most common issues:
There are 4 categories in this mode: Cleaning/Setting, Network/Internet, Microsoft applications, and Miscellaneous treatments.
All these categories contain short descriptions of the issues that DoktorKleanor knows how to fix. Just check the boxes corresponding to the issues you are experiencing, then click on "Start selected treatments."

The first category, Cleaning/Setting, has additional options as its name implies : you can set the disk spin down delay, launch MacOS X's maintenance tasks, delete additional languages and clear the list of recent folders in the Finder's "Go" menu.
Preferences that revert to defaults depending on treatments:
Apprentice mode: no preferences revert to defaults.
Wizard mode:
Safari is unstable:
Issues with Mac Help:
Find by content is very slow:

Word won't let you choose another font:
Drag & drop no longer works:
Light:
Full (in addition to the preferences mentioned in Light):
Default browser setting does not stick:
Running DoktorKleanor is simple. Check the boxes that correspond to the problems you are experiencing, and let the Doktor do its stuff. However, before any attempt at troubleshooting your Mac, DoktorKleanor's developers recommend using Disk Utility (First Aid tab) to fix possible disk problems. Sound advice.
DoktorKleanor is one of the most interesting of these utilities, with a lot of useful features and a very intuitive interface.
System requirements:
Doktor Kleanor is freeware.
MacJanitor is designed to be used on a periodic basis by Mac OS X users who don't leave their computer on (and awake) 24 hours a day. MacJanitor is provided as freeware as a service to laptop and energy-conscious home users.

The Unix subsystems on Mac OS X were originally written for machines that were typically never shut off. Mac OS X inherits this assumption and has many system maintenance tasks that are scheduled to run between 3 a.m. and 5 a.m. In addition, there are scripts designed to run weekly on weekends, and others that run once a month in the middle of the night.
If these maintenance tasks are never run (such as on a laptop that is always shut off at night), many log files and system databases will grow extremely large or fail to get backed up.
My Mac is occasionally powered up at 3 a.m., but only when Iím using it. Iíve always made a habit of putting my Macs to sleep or shutting them off when they are not in use, so Iím a likely candidate for MacJanitor.
MacJanitor provides a way to run these system tasks at the click of a button. Laptop users could click the "daily" button every morning (or every few days), or office workers could click the "weekly" button on Mondays.
If you've been leaving your machine off at night without allowing the maintenance tasks to run for several weeks or more, the first time you run them using MacJanitor may take several minutes. Also, if your log files have grown extremely large and you are low on disk space, the tasks may have problems moving the files around and compressing them. After that, it typically takes less than a minute for each task. I didnít sit and watch MacJanitor do its stuff, but it was all done when returned after a short break.
The output of the task is displayed in the scrolling view in the bottom part of the window. If for some reason you feel the need, you may print the output of the system maintenance tasks (but why?).
You can't really hurt anything by running the tasks more frequently than intended, and they don't need to be run on a strict schedule. Just run them periodically when you get a free minute every few days or weeks.
New in this version:
This is a very useful little tool - the choice for minimalists.
MacJanitor is freeware.
Panther Cache Cleaner is yet another a utility designed to provide easy access to numerous OS X maintenance and utility options. When used in combination with OS X's disk repair tools, it can be very effective in curing many system problems.

Panther Cache Cleaner helps simplify system maintenance chores with an easy point and click interface to many OS X functions. Panther Cache Cleaner can improve system performance by tuning Internet and file caching settings and by implementing ram disks. Panther Cache Cleaner can improve startup performance by eliminating duplicate or orphaned Login Items.
PCC Documents and the PCC Engine can help maintain system health by providing set and forget automation of common maintenance chores Used as directed, Panther Cache Cleaner can be a powerful tool to keep OS X running smoothly.
PCC has a nice Panther icon, but its user interface is a bit stark and unimaginative compared with the snazzy OnyX, for example. However, the functionality is there for several dollars cheaper than all but one of the shareware competitors.
Features
New in this version: Version 2.1 of PCC is all new and updated for OS X 10.3. This release adds the ability to repair root directory OS X symbolic links. It adds the ability to recreate the OS 9 Desktop alias. It adds the ability to enable the Panther Expose Blob. This release adds new Login Items management tools. PCC can scan Login Items and remove or relink orphaned entries. It offers the ability to scan and remove duplicate entries from the Login Items. This release enables a Login Items folder similar to the Startup Items folder of the classic Mac OS. This folder resides in the home directory, and any documents, folders, aliases, app, etc. will be launched at login. When active, PCC will treat the System Preferences Login Items and the Login Items folder as a single pool of login items. Duplicates and orphans are scanned across both sets. This release also includes some minor bug fixes and improvements. This release is a free upgrade for previously registered Panther/Jaguar Cache Cleaner users.
System requirements: Mac OS X 10.1 or later with BSD subsystem
Panther Cache Cleaner is $7.95 shareware
The developer of the famous TinkerTool Finder and Dock utility that provides GUI access to certain hidden preferences in OS X has jumped in with another system maintenance utility dubbed TinkerTool System, which is Euro 7.00 demoware.

TinkerTool System allows you to change advanced operating system settings and gives access to internal maintenance features built into Mac OS X. The following features are available in TinkerTool System:
The features marked with an asterisk (*) are available without any restrictions even if TinkerTool System runs in demo mode. In demo mode, TinkerTool System lets you check out the other features, but you need to register in order to apply them.
TinkerTool System is fully compliant with Apple's security guidelines for Mac OS X. It does not need an installer and does not require special system packages to be installed. To launch the tool, no administrator password is needed.
System requirements: Mac OS X 10.2.3 or later
TinkerTool System is Euro 7.00 Shareware (not to be confused
with the basic TinkerTool which continues to be freeware).