EDIT 2012-12-15: With the Retribution AI, using bombers for ninja exploration is still possible but much more expensive. See this post for details.
Increasingly awesome title edition~
Alas, this is the end of the 0.0 ninja series unless I find something else to do there. That probably will not happen in the near future.
In terms of isk/hour, 0.0 exploration is pretty much the best money in the game. It is a fairly specialized profession, and not many people do it -- you need the right ships, the right skills... and you need space to do it in, or so many people think.
This guide will describe a method for doing limited 0.0 exploration with only cloaky ships. Using it you will be able to drive out to the edge of the galaxy, grab a billion isk of exploration loot, and drive back to jita, all in essentially perfect safety.
This guide is specific to guristas because they are what I'm familiar with, but the methodology should be adaptable to other factions (especially serpentis).
This method relies on dual boxing two cloaky ships, a tank and a damage dealer.
The tank is a nullified, cloaky tengu which scouts, scans, and tanks, set up similarly to my old 'worst tengu fit ever' exploration utility fit.
The damage dealer is a stealth bomber. These do excellent damage for their size, have a cov ops cloak, and can hit out to 60 km with t1 torpedoes.
It goes like this: The tengu goes first, since it is much more likely than the bomber to survive a gate camp. You take the ships out to 0.0, find safe systems, and scan down sites. Once an appropriate site has been located the tengu warps in first and pulls all the aggro, the bomber follows, and they get to work. Just watch local and d-scan for hostiles dropping probes.
How far you go into 0.0 is up to you. Any system that doesn't have something nasty on d-scan is usually fine, though in systems with heavy traffic or people in local it's more likely someone will try to scan you down. The further you go from empire and pipes, the less likely it is you'll be interrupted. Personally I'm quite fond of tenal.
I just do day drips, since I have to go return to highsec on a near-daily basis, but operating out of an NPC station where you can buy ammo would really streamline the process.
Doing a site
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Without further ado...
If your skills aren't awesome enough to be cap stable with that, you can totally switch out the boost amp for a cap recharger. It just means sometimes it will be necessary to orbit with the AB on to reduce incoming damage.
In the tengu's cargo you should carry about 6000 heavy missiles, then fill the rest with torpedoes to resupply the bomber. This should result in both ships running out around the same time.
If you don't feel like training astrometrics 5, you can switch the t2 probe launcher for a sisters probe launcher.
Also of note, I strongly disrecommend using any ship other than a tengu for this. Fast align time is key to a T3 surviving gate camps in 0.0, which means armor tanks (proteus, legion) won't work, and the loki has slower align time and a much worse tank. The tengu will definitely work for caldari and gallente damage types, and non-caldari rats are said to be much easier to tank so it may also be able to handle minmatar or even amarr; however, I haven't tested these.
EDIT: It is actually possible to get the loki align time down to just 0.1 second slower than the tengu, and for sanshas damage it has a better tank.
The second target painter is nice, but with cov ops 4 it isn't really necessary unless you're shooting cruiser hulls or elite frigates a lot. If you want to drop one for a salvager, analyzer, or MWD you can. Archaeology and salvaging sites are pretty worthless, in my experience, but salvaging dread guristas is sometimes worth a few million and an MWD would be really helpful if you do end up jumping into a gate camp (see evading gate camps in a cov ops ship).
EDIT: You can also fit a MWD by using a kmb-50 implant, which adds 3% CPU and costs 22 mil. Worth it.
The codebreaker is for ladar hacking sites (see H-PA Crash Crew), which are fast, easy, and can drop the nanite control skill book, which is worth about 250 mil. Except for drone regions, all or nearly all 0.0 regions have ladar hacking sites.
We use a manticore here because it receives a bonus to kinetic damage, which is best for guristas rats. You will want to match the bomber to the type of rats you're shooting.
This method severely limits the types of sites you can do. Sites which do AOE damage (e.g. guristas military complex) are completely out of the question. Sites which have multiple spawns, which may target the bomber, (most hacking and salvaging sites) will be very tricky. Sites where you have to kill large numbers of elite frigates or cruisers (e.g. guristas fortress) will run you out of torpedoes after only a few sites. Sites that the tengu can't tank (maze) will just plain kill you.
So what does this leave us?
Fascinatingly, with guristas this removes almost all the worthless sites, and fewer than half the high value ones. We are left with four easy, predictable, high value, and fairly common sites: DED 6/10, 7/10, and 8/10, plus LADAR hacking sites. We'll just have to see what sort of earnings these sites can provide for us.
So, does it work? Well, so far I have spent 19.4 hours doing exploration this way, and retrieved 2440 million isk worth of loot. This comes out to 125m/h.
(This figure does not include travel time to/from jita; or bounties, which I estimate totaled a hundred million or so)
Due to the highly variable nature of exploration income, 19 hours is not enough to take an accurate baseline. However, I have extremely extensive experience with guristas exploration, and my feeling is that this figure is pretty reasonable.
EDIT: After doing several more runs of this and tracking isk/hour in a general sort of way, and after the release of deadspace invulnerability fields, I think that figure might be somewhat low. Figure more than 125, but definitely less than 200.
It's profitable, easy, and mostly safe. I feel confident that the long term isk per hour is higher than that of a pretty good highsec incursion fleet, and personally I find it much more enjoyable than incursions. Intermittent and randomized rewards mean it feels like less of a grind, standard rats don't switch targets so you don't have to be paying attention every second, and there are no fleetmates or FC to worry about. Plus, there's just something very relaxing about a quiet 0.0 system. Maybe I've spent too much time out there, but highsec and low are just too cramped for me to ever feel comfortable.
Also, excitement! Sometimes people try to kill you and stuff!
tl;dr more money, more fun, more interesting