How do I most efficiently maintain my weapons in System Shock 2?

To clarify terminology, repair tools are used to repair broken/jammed weapons, while maintenance tools are used to improve the condition (0-10 rating) of weapons.

Putting points into Maintenance skill will give you more bang for your buck from maintenance tools; a certain level of Maintenance skill is also necessary to be able to maintain certain weapons. You can also minimize the amount of repairing you have to do by opting to use melee weapons instead of guns when possible.

If this still gives you trouble and/or you just don't want to deal with it (which I can certainly understand!), it's also possible to reduce or disable weapon degradation by editing user.cfg in your game's install directory (creating it if there isn't already one) and adding the following line:

gun_degrade_rate <n>

...where <n> is a number between 0 and 1: 0 disables degradation entirely, while 1 degrades at full speed. (For example, 0.5 would degrade at half the normal rate.)

Patched versions of the game will contain a document called readmep.wri in their root install directory that provides more information.