1) Use a Firewall

Make absolutely sure that your server has a firewall running all the time. A firewall is like a screen door to your porch. It blocks out flies, rodents and other pests but you can still walk out and use your BBQ. If someone ever were to get into your server, which is very very likely, the first thing they’re going to try and do is upload something to start a daemon or their own service like an IRC server or use a port to launch attacks to other systems. A firewall with egress and ingress protection can stop both incoming and outgoing attacks even when you’re not aware of it. We recommend using APF on Linux systems or TinyFirewall on Windows Servers. These are software firewalls so there’s no extra monthly cost like a hardware firewall. For very busy systems a hardware firewall is recommended so it takes the burden off your system CPU/RAM and resources to do the work.

Know what ports are open and why, know how to block and unblock an IP. These are basic things you need to understand in the daily security of your system. If someone from an IP begins a brute force attack you want to know how to stop them, right away.

2) Update your kernel and OS

Make sure your server is using current, updated software. Use the stable version which has been tested more than any beta and update as soon as possible. An old kernel can lead to an easy target for your server. If you’re not sure then ask your provider for the latest update.

3) Monitor Logs

Do you know what logs record which activities? How often are they updated and rotated?
LogWatch is a great tool to email you the daily reports of your systems activity of anything it determines unusual, EG repeated failed logins. Besides using this you should check your logs manually to see what’s up. Tail –f /var/log/messages and view your Apache logs as well.

4) Backups
I still never understand why no one backs up their data yet you spend hundreds of hours working on your website or application then you absolutely must have a second hard drive for backups or use a remote back up system or a combination of these.

5) Limit Access to a Minimum

Do not give users more access than the absolute minimum they require. Never give them shell access, restrict file access to a bare minimum and leave other services turned off by default until specifically requested and you determine that its safe to do so.

6) Lock down PHP and use Mod_Security with Apache

PHP is actually a large security risk but there are a few things to do to help lock it down. CGI has Suexec,which helps runs proccesess as the user and PHP has something similar called PHPSuexec but there are a few downfalls. You should also use open_base directory protection, have safe_mode on system wide, turn off register_globals, enable_dl and allow_url_open to help lock things down further.
You can use server wide protection with mod_security, a web server filter that can watch all requests to see if they match a rule and react by logging, denying the request or other programs. I highly recommend this on Apache based servers and can be extremely useful in blocking attacks and stopping hackers before they do any damage. Mod_Security Installation

7) Lock /tmp /var/tmp and /dev/shm partitions

On Linux each partition can have certain access restrictions. Since /tmp /var/tmp and /dev/shm are world writable directories they’re often home to uploads, sessions storage and hacker executables. Since anyone can read-write-excute anything from these directories it becomes a major security concern. With /etc/fstab however you can limit what can be done in these locations. If you see defaults beside the /tmp line remove it and replace it with noexec,nosuid this will stop any executables from being allowed to run. Do the same for /dev/shm and make /var/tmp and shortcut (symbolic link) to /tmp.

8 ) Intrusion Detection System (IDS)

An intrusion detection system or IDS is like a burglar alarm on your server. It keeps a record of which files were changed when and alerts you of anything new or altered. This is critical because hackers usually try to replace binary applications like ps, top, netstat and others. This means when you run this new version of ps or top to see processes running they make it so it actually HIDES their hacker software, even though its running it won’t show up. Some IDS systems include TripWire, Snort and AIDE. Chkrootkit installation

9) Review Processes Running and Remove Extra Software

You can’t protect a system if you don’t know what’s on it. If a hacker adds an extra process that you see in PS but you wouldn’t notice if you didn’t know what should be there usually. Know what runs on your system and why which user. How does Perl or Apache run, under which user? You can check your processes usually with top or ps auxfww which gives you a tree view. Check these every time you login to your server.

10) Keep an Eye on the Servers Performance

Know what speed your server is running at and how much bandwidth it uses on a daily basis. If an attacker compromises your system and you don’t know you’ll probably notice the system responding slowly or using a lot of bandwidth. If you don’t know what your system is usually like how will you notice something out of the ordinary. This is all common sense but some people never bother to check until they ask their provider after a system has been slow for 2 weeks

Knowing your system makes you one step ahead of an intruder. Check it often and ask an expert if you’re ever over your head. There are MANY other things you can and should do to ensure your server is secure but these are a few basics that everyone should use.

REF : whmdestek.com forums.