Q: Apps and Utilities not opening after Clean Up

First, delete "CleanApp" and never install it or anything like it again.

If you don't already have a current backup, back up all data, then reinstall the OS. You don't need to erase the startup volume, and you won't need the backup unless something goes wrong. If the system was upgraded from an older version of OS X, you may need the Apple ID and password you used to upgrade.

There are ways to back up a computer that isn't fully functional. Ask if you need guidance.

If you installed the Java runtime distributed by Apple and still need it, you'll have to reinstall it.

Good question:

Also, why do you advise against things like CleanApp?

Obvious answer:

Hi, i've just been doing a bit of a clean up on my mum's iMac, and now most of her apps and utilities aren't opening. I was using CleanApp to get rid of applications and other stuff

There are a raft of these apps out there that promise to "clean", "tune up" "speed up" or whatever your Mac. They're unnecessary, first, and more importantly, can do a lot more harm than good. Are you sure what happened is user error?

How to maintain a Mac

1. Make redundant backups, keeping at least one off site at all times. One backup is not enough. Don’t back up your backups; make them independent of each other. Don’t rely completely on any single backup method, such as Time Machine. If you get an indication that a backup has failed, don't ignore it.

2. Keep your software up to date. In the Software Update preference pane, you can configure automatic notifications of updates to OS X and other Mac App Store products. Some third-party applications from other sources have a similar feature, if you don’t mind letting them phone home. Otherwise you have to check yourself on a regular basis. This is especially important for complex software that modifies the operating system, such as device drivers. Before installing any Apple update, you must check that all such modifications that you use are compatible.

3. Don't install crapware, such as “themes,” "haxies," “add-ons,” “toolbars,” “enhancers," “optimizers,” “accelerators,” "boosters," “extenders,” “cleaners,” "doctors," "tune-ups," “defragmenters,” “firewalls,” "barriers," “guardians,” “defenders,” “protectors,” most “plugins,” commercial "virus scanners,” "disk tools," or "utilities." With very few exceptions, this stuff is useless, or worse than useless. Above all, avoid any software that purports to change the look and feel of the user interface.

The more actively promoted the product, the more likely it is to be garbage. The most extreme example is the “MacKeeper” scam.

As a rule, the only software you should install is that which directly enables you to do the things you use a computer for — such as creating, communicating, and playing — and does not modify the way other software works. Use your computer; don't fuss with it.

Safari extensions, and perhaps the equivalent for other web browsers, are a partial exception to the above rule. Most are safe, and they're easy to get rid of if they don't work. Some may cause the browser to crash or otherwise malfunction.  Some are malicious. Use with caution, and install only well-known extensions from relatively trustworthy sources, such as the Safari Extensions Gallery.

Never install any third-party software unless you know how to uninstall it. Otherwise you may create problems that are very hard to solve.

4. Beware of trojans. A trojan is malicious software (“malware”) that the user is duped into installing voluntarily. Such attacks were rare on the Mac platform until sometime in 2011, but are now increasingly common, and increasingly dangerous.

There is some built-in protection against downloading malware, but you can’t rely on it — the attackers are always at least one day ahead of the defense. You can’t rely on third-party protection either. What you can rely on is common-sense awareness — not paranoia, which only makes you more vulnerable.

Never install software from an untrustworthy or unknown source. If in doubt, do some research. Any website that prompts you to install a “codec” or “plugin” that comes from the same site, or an unknown site, is untrustworthy. Software with a corporate brand, such as Adobe Flash Player, must be acquired directly from the developer. No intermediary is acceptable, and don’t trust links unless you know how to parse them. Any file that is automatically downloaded from a web page without your having requested it should go straight into the Trash. A website that claims you have a “virus,” or that anything else is wrong with your computer, is rogue.

In OS X 10.7.5 or later, downloaded applications and Installer packages that have not been digitally signed by a developer registered with Apple are blocked from loading by default. The block can be overridden, but think carefully before you do so.

Because of recurring security issues in Java, it’s best to disable it in your web browsers, if it’s installed. Few websites have Java content nowadays, so you won’t be missing much. This action is mandatory if you’re running any version of OS X older than 10.6.8 with the latest Java update. Note: Java has nothing to do with JavaScript, despite the similar names. Don't install Java unless you're sure you need it. Most people don't.

5. Don't fill up your boot volume. A common mistake is adding more and more large files to your home folder until you start to get warnings that you're out of space, which may be followed in short order by a boot failure. This is more prone to happen on the newer Macs that come with an internal SSD instead of the traditional hard drive. The drive can be very nearly full before you become aware of the problem. While it's not true that you should or must keep any particularpercentage of space free, you should monitor your storage consumption and make sure you're not in immediate danger of using it up. According to Apple documentation, you need at least 9 GB of free space on the startup volume for normal operation.

If storage space is running low, use a tool such as the free application OmniDiskSweeper to explore your volume and find out what's taking up the most space. Move rarely-used large files to secondary storage.

6. Relax, don’t do it. Besides the above, no routine maintenance is necessary or beneficial for the vast majority of users; specifically not “cleaning caches,” “zapping the PRAM,” "resetting the SMC," “rebuilding the directory,” "defragmenting the drive," “running periodic scripts,” “dumping logs,” "deleting temp files," “scanning for viruses,” "purging memory," "checking for bad blocks," "testing the hardware," or “repairing permissions.” Such measures are either completely pointless or are useful only for solving problems, not for prevention.

The very height of futility is running an expensive third-party application called “Disk Warrior” when nothing is wrong, or even when something is wrong and you have backups, which you must have. Disk Warrior is a data-salvage tool, not a maintenance tool, and you will never need it if your backups are adequate. Don’t waste money on it or anything like it.