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I am running a Minecraft Server and a Web Server and I do have a big list of packages, that I might need to update.
How safe it is and is it a regular normal practice to update prompted packages for your dedicated server?

acpid Advanced Configuration and Power Interface event daemon New version 2.0.7-1squeeze4 Squeeze
base-files Debian base system miscellaneous files New version 6.0squeeze5 Squeeze
bind9-host Version of 'host' bundled with BIND 9.X New version 9.7.3.dfsg-1~squeeze5 Squeeze
dnsutils Clients provided with BIND New version 9.7.3.dfsg-1~squeeze5 Squeeze
file Determines file type using "magic" numbers New version 5.04-5+squeeze2 Squeeze
host Transitional package New version 9.7.3.dfsg-1~squeeze5 Squeeze
initscripts scripts for initializing and shutting down the system New version 2.88dsf-13.1+squeeze1 Squeeze
libapache2-mod-php5 server-side, HTML-embedded scripting language (Apache 2 module) New version 5.3.3-7+squeeze9 Squeeze
libapr1 The Apache Portable Runtime Library New version 1.4.2-6+squeeze4 Squeeze
libbind9-60 BIND9 Shared Library used by BIND New version 9.7.3.dfsg-1~squeeze5 Squeeze
libdns69 DNS Shared Library used by BIND New version 9.7.3.dfsg-1~squeeze5 Squeeze
libisc62 ISC Shared Library used by BIND New version 9.7.3.dfsg-1~squeeze5 Squeeze
libisccc60 Command Channel Library used by BIND New version 9.7.3.dfsg-1~squeeze5 Squeeze
libisccfg62 Config File Handling Library used by BIND New version 9.7.3.dfsg-1~squeeze5 Squeeze
liblwres60 Lightweight Resolver Library used by BIND New version 9.7.3.dfsg-1~squeeze5 Squeeze
libmagic1 File type determination library using "magic" numbers New version 5.04-5+squeeze2 Squeeze
libssl0.9.8 SSL shared libraries New version 0.9.8o-4squeeze13 Squeeze
libxi6 X11 Input extension library New version 1.3-7 Squeeze
libxml2 GNOME XML library New version 2.7.8.dfsg-2+squeeze4 Squeeze
openssh-client secure shell (SSH) client, for secure access to remote machines New version 5.5p1-6+squeeze2 Squeeze
openssh-server secure shell (SSH) server, for secure access from remote machines New version 5.5p1-6+squeeze2 Squeeze
openssl Secure Socket Layer (SSL) binary and related cryptographic tools New version 0.9.8o-4squeeze13 Squeeze
php5-cgi server-side, HTML-embedded scripting language (CGI binary) New version 5.3.3-7+squeeze9 Squeeze
php5-cli command-line interpreter for the php5 scripting language New version 5.3.3-7+squeeze9 Squeeze
php5-common Common files for packages built from the php5 source New version 5.3.3-7+squeeze9 Squeeze
php5-mysql MySQL module for php5 New version 5.3.3-7+squeeze9 Squeeze
procps /proc file system utilities New version 3.2.8-9squeeze1 Squeeze
python interactive high-level object-oriented language (default version) New version 2.6.6-3+squeeze7 Squeeze
python-minimal minimal subset of the Python language (default version) New version 2.6.6-3+squeeze7 Squeeze
sudo Provide limited super user privileges to specific users New version 1.7.4p4-2.squeeze.3 Squeeze
sysv-rc System-V-like runlevel change mechanism New version 2.88dsf-13.1+squeeze1 Squeeze
sysvinit System-V-like init utilities New version 2.88dsf-13.1+squeeze1 Squeeze
sysvinit-utils System-V-like utilities New version 2.88dsf-13.1+squeeze1 Squeeze

On a dedicated machine, I expect this to work just fine. But, to be completely safe, I always recommend backing up your critical files before applying system updates, as well as periodically as a matter of course.

Maybe, there is some special program, that you know about, that is designed to back-up all the critical system files for me?

You should really only need to back up files that you've uploaded or changed (such as server configuration files and databases).

Sounds like linux is not properly unorganized or not designed for easy backup&restore job. I mean, I will have to create a script, but first I will have to like remember each single file, I've changed, which is impossible for average human being.
Kinda disappointing.

You're leaving me scratching my head, because that's normal for all systems.

I'm sure you can search around and find some backup software, but usually it's easier to just save the few files that you can't replace.

This is how I do things on my linux box. Running a full backup is usually a pain. I usually do backups with a cron job and just backup the folder I want (in my case, the web directory)

sorry, I mean "not [] []organized [that well]".