Preventing Science Fiction Catastrophe
1) Don't put windows on the Bridge, and locate the Bridge somewhere deep within the ship where it won't be crippled if something slams into the front. Why do we have windows when embedded cameras get the same effect while being far more resistant to damage?
2) Enable text messaging. If you have very poor reception, every byte counts; a brief text message can be received much more readily in areas of poor reception. Best of all, it arrives whether or not you happen to be near the transmitter by the time the receiver can hear messages. Just make sure it's encrypted, or else anyone else can pick it up, too.
3) Put solar paneling on everything you reasonably can, or take a solar recharger with you. For that matter, always have an alternate method of charging everything when the 'main system' is offline, including the spacecraft, and include backups for essential systems (like, say, antimatter containment and life support). There is no excuse for losing power barring catastrophic damage or carelessness, and there is no excuse for not providing safety fallbacks for essential systems barring flat-out negligence.
4) Energy weapons are expensive. Bullets are cheap. Advanced machining technologies allow for the best possible craftsmanship on a non-electronic firearm, while advanced propellant technology, electronic firing pins, and caseless ammunition allow heavy fire at significantly lower energy costs than your average plasma weapon. As a fallback weapon, as a stealth alternative, or as a cost-saving measure, projectile weapons are still useful.
5) Computers have security levels, antivirus programs, and other systems in place to make sure that even a competent hacker has to have appropriate tools in order to bypass them. If an intelligent twelve-year-old can format the computer's hard drive or change the system's programming by messing with it unattended for a few minutes, your system has less security than a display laptop at Wal-Mart.
6) Always keep backups, plural. Aside from having backups of important data, regular backups of the entire computer system should be kept, and an emergency reinstall option should be ready in case the backups are hopelessly corrupted and the entire system has to be restored to factory default condition. Any changes in configuration should be noted and stored as part of the backups. The backup options should not be kept all in one place where they can be easily stolen or destroyed, either.
7) Every security system is prone to fail in edge cases, either failing by becoming insecure or failing by becoming too secure to function. One person has the key? What happens when that person goes missing or is killed? All changes require a core password? What happens if the password is forgotten? Computer only responds to human crew members? What happens if the computer no longer recognizes the crew? By thinking out the what if scenarios, you can determine an acceptable level of security, hopefully with solutions to at least some of the edge cases you will inevitably encounter.
8) Bypassing is meant to be complex; basic operation is meant to be simple. Assuming you have an appropriate user with an appropriate key, they should be able to access the system with less difficulty than an unauthorized intruder. Again, if your systems can be accessed by a bored twelve-year-old more easily than they can by your actual crewmembers, your security system needs improvement.
9) If you have a device capable of recreating a fallen crewmember based on a brain scan and genetic code, there is no reason for your backups of crewmembers to be any less stringent than your backups of astrogation software and personnel files. While there are ethical arguments against creating multiple operating clones of a single individual, it is generally wise to have a backup of your most competent engineer in case he gets eaten by the Monster of the Week, and it saves an enormous amount of hassle in finding new staff if you can simply respawn the old ones with an admonition to avoid whatever killed them last time.
10) If possible, there should be publicly known caches of emergency supplies throughout the ship/station/etc where they can be easily found and used in the event of an emergency. Nothing is as embarrassing as losing five crewmembers to vacuum because nobody had the materials to temporarily patch the hole or the equipment to survive in vacuum.
11) Also if possible, there should be private caches of emergency supplies for use by ranking officials/security officers/the commander in a crisis that are not publicly identified, such that if the entire crew mutinies, they won't be able to find and take all of the survival equipment and weaponry with them.
12) If your computer harbors an AI of any kind, it is wise to treat it with politeness, listen to what it has to say, and explain your reasoning when you contradict its recommendations. Not only will this be helpful in preventing the AI from going rogue, but it will force you to consider your plans more carefully and look for alternatives where possible, rather than fixating on one plan and carrying it through to conclusion regardless of future events or information.
13) Do not rely too heavily on one technology, piece of equipment, or weapon. It's one thing to find yourself out of alternatives if everything fails at once; it's another to find yourself out of alternatives because the only option failed. Improvising beautifully is no excuse not to have more than one plan in the first place.