It's simple: Skybase, Underground, or on land. (I'm making myself a new base; keep in mind that I have 30plus factions members I need to fit in a house xD)
Make your base under ground! It makes it hard to find, if people are using x-ray they will usually find it, but if you manage to find a spot with a lot of coal or other things like that, you will be fine
Underground. Almost impossible to TnT cannon into without using a LOT of TnT, pour lava over it to protect from xray, and be sure to make it big enough to house all of your faction members.
Skybases are probably the second most vulnerable base (The first being a land base, it's both easy to find and easy to get into). In 1.2.5 (Full release, not beta) it would be wise because back then it was a very new type of base, people didn't really look up in the sky. Nowadays, people turn their clouds off and always. On non-faction servers people hide little vaults (not their main base, just a couple storage base) in the sky, and their vault is literally just chests for a floor and one on each side of it so they don't fall. But in factions they would notice the claimed land and go searching.
What I do is build it in the ground then put obsidian all around that, then put water on top of the obsidian.
You don't need water on top of obsidian, that's just a waste of iron/buckets. Heck, if yo build it not next to a cave and far enough underground it is impossible to tnt cannon even without obsidian.
But then I can get hybrid tnt cannoned? (A tnt cannon that shoots sand and tnt making the tnt able to explode in the water)
You can use cobble covered in water until you have enough $$ to make a second layer of obsidian. More important than TNT cannons on this server, you have to make your base /jump proof. Double thick walls will help with that. Redstone repeaters (an important part of popular TNT cannons) are disabled in factions, but I've been playing around with a hybrid cannon design that does not use them
Did, I left the server for about a week to study for my PSAT's. When I returned we got raided; I mean how do you from 300 power+ to -200power. I was greatly disappointed.