Minecraft wiki entry for Multiplayer_PvP_bases, associated text: If you want to keep people not in your faction out of an area of your base, put doors in front of it. Allied faction members can't open doors unless they have pressure plates in front of them.
Read up on historical military strategies. Although they're from real life, many principles still apply to factions warfare and may just help you outsmart the competition.
Ally, ally, ally! You don't have to fight everyone. Make some friends as you go. Conquest is always more fun when it's shared with good friends.
Obsidian is essentially bedrock in claimed areas, unless the server has a plugin that lets it be blown up.
Your defense is only as strong as its weakest link. Any weak spots in your defenses WILL be found by your enemies, and it WILL be exploited so much it will boggle your mind. One missing block of obsidian or one mine that isn't claimed at the entrance and sealed off by a door can be your downfall.
You'll most likely forget to obsidian the floor when you're obsidian covering your base. It's an easy mistake to make. Make sure you do that. Otherwise, raiders can dig up through the floor of your base.
If you wish to have a way out of any sticky situations with other players, a hidden nether portal transport like the kind referenced earlier can be used as a quick escape route. Since 1 block in the nether is a greater distance than in the overworld, if worst comes to worst, you can activate your hidden piston door, head through your portal, and run down a corridor to get away from your opponents quicker than they can catch up to you, assuming they don't find your portal. You can also use minecarts (or a human cannon) for this.
Experiment! Combine anti-griefing techniques together! Use a boat/minecart to transport an elder guardian through nether portals, into a 5-block-thick obsidian bunker surrounded by lava and half-open wither cages, placed on top of the nether! This definitely will stop all the raiders in the world!