There are a few category's of files: Protection, Attacking, Utility Software, Money Files, and Viruses.
These pieces of software are used to attack others and gain control of their system. Be careful though as doing so might reveal your IP and leave you open to attack.
Waterwalls (.wwl ver 0.5 to 5.7) :
This is one half of the most important pieces of software in the game. It's used along with a password cracker (which we'll discuss later) to break into remote systems. Normally, a cracker alone will work but if the person who owns the system you're attacking (or the NPC) is even a little advanced in the game, there will most likely be a firewall. In order to bypass this and successfully crack a password, you need a waterwall of equal or higher level than the firewall that is running on the system you're attacking. A version of the waterwall software is kept on the external harddrive of virtually every single player in the game. Don't leave your box without one. The higher the version you have, the more systems you can break into and the time taken will also decrease (depending on your CPU and level of cracker). If you are inside someones system where a firewall is running and someone deletes all of the waterwalls you have that are equal to or higher than the firewall running on a system, you get kicked from it.
Password Crackers (.crc ver 0.3 to 5.2) :
This is the other half of the most important software in the game. You abolutely NEED this software, even more so than a waterwall file. This will work on it's own as long as their isn't a firewall running on the other system. Unlike the waterwall file, it isn't necessary to have a higher level to break into higher levels of firewalls but it helps. The better your version is (along with your waterwall file and your CPU) the faster you'll be able to crack passwords. While waterwalls are on "virtually" every single players external harddrive, I feel confident in saying that the cracker is on EVERY active players external. It is an absolute must have.
DDoS Remote (.rddos ver 0.3 to 1.0) :
This is used to control your "botnet". A botnet is a collection of VPCs/NPCs which you have infected with a DDoS virus which is used to attack other systems. It takes 30 seconds per VPC/NPC with a minimum of 5 "slaves" to attack. If you plan to be any kind of DDoSer, this is a necessesity for your external harddrive.
These pieces of software are used to prevent attacks or remove viruses left by them
Firewalls (.fwl ver 0.5 to 5.7) :
This is a very handy piece of software. It is used to protect your VPC from attacks (although no system is 100% secure) and reduce the damage taken by a DDoS hit. Keep your highest firewall unhidden and unencrypted at all times as it will no longer prevent people from getting access without a waterwall. A handy little feature for firewalls (if you can pull it off) is using them to boot people from your system. If someone has managed to hack you and they have taken out your firewall(s), get someone to upload you one higher than the attackers waterwall (or just have them delete the attackers waterwalls) and they'll instantly be kicked, rendering you temporarily safe.
Anti-virus (.av ver 0.3 to 4.9) :
This is used to clean viruses from the system it's currently running on (be it your own or a remote system). It will completely remove any virus that is of equal or lower level than it and will simply deactivate any that are higher (with the exception of .vtrack). Running one can be a bit of a pest, even if it doesn't remove the virus completely as deactivating it will stop those who installed it from being able to let it build up a decent amount of money for collection. A tip for using an AV...using it along with a password reset removes you from someones slavelist, givin the impression you reset your IP. Handy for tricking people.
These are used for three things. Gaining repuation, gaining money and gaining slaves for use as a botnet to attack others and they all have the same icons.
Uninstalled virus -
Installed virus -
Spam virus (.vspam ver 0.3 to 4.9):
The spam virus is used to send out spam e-mails. This generates more repuation than euros but will give both.
Warez virus (.vshare ver 0.3 to 4.8):
The warez virus is used to sell warez files (.rip). Both must be on the VPC/NPC in order for it to work. This virus will generate more money than repuation but like the spam virus, it gives both.
DDoS virus (.vddos ver 0.3 to 1.0):
This is the virus used in conjunction with the .rddos applicaton. You need to have this installed on a minimum of five different VPCs/NPCs to launch an attack and like previously stated, it takes 30 seconds per slave. Each DDoS hit launched produces a small amount of rep per slave but no euros.
Tracker Virus (.vtrack ver 0.7):
This virus is used in conjunction with a domain name to track the IP changes of a VPC. If someone resets, wait for the tracker to update, visit the domain and it'll take you to the new IP. Best used with a hider once a seeker is deleted so people won't run an AV or format and it leaves lines in logs so be sure to hide those logs until you can't do it anymore. The logs appear roughly every 10/15 mins when the virus updates the IP to the domain.
These pieces of software are used to collect the reputation/money generated by your spam or warez viruses.
Mailer (.mailer ver 0.3 to 4.9) :
This is used alongside your spam viruses to "collect". As previously stated, it gives more repuation than money but will accumulate both.
FTPcash (.fc ver 0.3 to 4.8) :
This is used alongside your warez viruses to "collect". Again, as I said previously it is the opposite of spam and will provide more money than reputation. For this to work, it needs one of the .rip files on the NPC/VPC that the virus is installed on.
Warez (.rip ver 0.4 to 0.7) :
These files are sold by your Warez virus. You need to have a copy of one of these files uploaded to the target machine.
This is a collection of software which can help you in different ways. None are used exclusively for attacking or defending, they're just....helpful.
File Hider (.hdr ver 0.2 to 5.0) :
This is used to hide the presence of a file so that it can only be seen by someone running a "seeker" of equal or higher level. When you hide software, it can no longer be used...but you can simply redownload the file and it will replace the hidden one.
File Seeker (.skr ver 0.2 to 5.0)
This is used to unhide files that have been hidden. It is generally quicker than re-downloading but it depends on the connections of yourself and the place you are downloading as well as your CPU.
Analyzer (.ana ver 0.1 to 5.0)
This is used to check the hardware of the NPC/VPC you run it on. It must be uploaded to the target system and depends upon you having a maxed CPU to give the most accurate results.
File Encrypter (.enc ver 1.0 to 4.8)
This is used to encrypt a file. For the most part, this doesn't have a lot of uses other than for text files. Once encrypted, software can no longer be run until decrypted although, like hidden software, it cannot be over-written by re-downloading. If you can manage to encrypt some important peices of software on someones system without being caught, they have no choice but to delete the files or wait and decrypt them.
File Decrypter (.dec ver 1.0 to 4.8)
This is used to decrypt files that have been encrypted. There really isn't much more to say other than to explain that you need a decrypter of equal or higher level than the encrypter that was used to encrypt it.
Forum (.exe Unique/has no version)
This is used to host a personal forum on your group server. You have full admin privileges over it and it can be accessed by anyone who is inside the GS. If the file gets deleted from your GS, your forum will remain although you can't access it without reuploading the file.
Well that Pretty Much Explains it.