EVE Online at Ten Ton Hammer - Taking MMOG Gamers to the Next Level!

Only Fly What You Can Afford to Lose: This should be plastered on the login screen, if you ask me. Defensive war means losing ships repeatedly. You need to moderate your losses and take future attrition into account. Make sure that your warships are of a hull class which you can afford to lose. Flying one HAC, losing it, then going broke isn't going to save your alliance, but flying five battlecruisers and maintaining your balance might. If you have a particular ship that you're an expert at flying, make sure the fit is standardized such that you don't waste time dithering after you get blown up. Expect to die and don't be upset when it happens.

Don't Hoard: The natural tendency of players appears to be to have one station as a home base where assets and ships accumulate. In a conquerable station, this is a terrible habit. If your 'base' station is captured, you lose everything you've stashed in it. Keep a few (2-3 tops) combat ships which you've selected for affordability and efficiency in different stations in your space such that you can never be denied a combat vessel by a hostile camp. Keep clutter to a minimum; your extra loot should be regularly sold or ferried out to Empire or NPC 0.0.

Jump Clones: You should have Infomorph Psychology trained to four. Install a jump clone in each of the stations where you have a stash of combat ships. This will allow you to access your assets if the station is captured before you can evacuate, just in case. 

Cultivate Untouchable Income: Empire is a boring, terrible place, but having your income stream entirely dependent on 0.0 isn't wise if your alliance collapses. There are a number of ways which you can use your 0.0 earnings to set up backup income streams in Empire while times are good. Popular options: A PvE-fit battleship parked at a mission-running hub, an invention bpo/decryptor set, or a rack of four R&D agents constantly providing passive income from datacores. Make sure that you have one of these set up long before your alliance comes under stress, such that you can use your Empire income to fund your ship losses in defense of your space.

Anticipate the Enemy: As soon as your alliance comes under attack, you should commence researching your foe. Who are they, and more importantly, what do they normally do while on the offensive? Being surprised by the predictable is an act of criminal stupidity. As an example, Goonswarm recently got a hold of an account on Scorched Earth's forums and 'rushed' it, with many members logging in and posting offensive images (goatse.cx, etc). Scorched Earth members loudly expressed shock and horror, even though the exact same thing occurred to Scorched Earth's neighbor, Aggression, less than a week previously! Red.Overlord is infamous for camping jump beacons with battleship gangs or suicide capitals, so no one fighting them should be surprised when these tactics are deployed against them. Do your homework.

Chart the War Yourself: If something is going horribly wrong in your alliance, you can't trust your leaders to tell you; they'd probably prefer you not to know. You also can't trust the line members to tell you; odds are a lot of them don't keep track of things at the strategic level, and even if they do they might have been cowed into sycophancy. Charting the progress of a war isn't difficult, and the best way to judge if you need to make a quick exit is to figure it out yourself. Use Evemaps to chart sovereignty changes and keep a close eye on your alliance and corporate forums. Focus on strategic necessities like R64 moons, stations, and jump bridge networks. Come to your own conclusions, then compare those conclusions against the 'official line' being promulgated by the alliance leadership. In EVE, thinking for yourself is always the best defense.

If you keep your wits about you and keep an eye on the warning signs, even a total alliance collapse won't make much of a personal impact on you. The enemy is trying to destroy your assets to the point where you give up and quit EVE entirely; with a modicum of intelligence, you don't have to give him that satisfaction.