That is a very interesting question and one which there's constant research going into.
A few initial points. First, its becoming clearer and clearer that 'prokaryotes' is a very poor grouping to use for much of anything. The bacteria most of us think of are the smaller, faster-replicating members of the eubacteria. There's also the archaebacteria, which are deeply and fundamentally different from the eubacteria in their membrane composition, cell wall structure, DNA organization, and transcription machinery.
Second, it's becoming more and more clear that the eukaryotes are indeed the result of an early union of eubacteria and archaebacteria. I saw some very cool research at a conference last December bolstering the “eocyte hypothesis” - the idea that the Eukaryotic nuclear genome roots in one particular spot of the archaebacterial tree plus loads of horizontal gene transfer from the eubacteria that became the mitochondria. You can't root it there just by aligning things, this was long enough ago that base sequence is effectively randomized, you need to look at what sorts of proteins exist, characters that change very rarely as opposed to mere sequence, and its a very hard question that has required a LOT of sequence data from a LOT of organisms. Most of our DNA structure and transcription and some of our protein processing looks like the archaebacteria, but basically all of our metabolism looks like the eubacteria. This is interesting in the light of recent discoveries of symbiotic pairings of archaebacteria and eubacteria in nature in which they exchange metabolic products.
Anyways, the eubacteria and archaebacteria have deeply different transcription machinery and make their membranes in fundamentally different ways. Central carbon metabolism is all but identical though as is a lot of other pathways, and the core biochemistry. I've seen work proposing that the eubacteria and archaebacteria may have diverged before living things managed to synthesize their own membrane components rather than scavenging them from the environment. I've also seen interesting work to the effect that certain clay minerals can assemble fatty acids and other such membrane-building substances from acetate under the proper energetic conditions.
There's also a lot of diverstiy in DNA and RNA processing methods that isn't in any of the cellular life – there are truly bizarre ways of doing this that you only find in viruses. Viruses mutate incredibly rapidly and so you cannot try to root them anywhere, they change too fast. That being said there are proposals that they may be primordial, elements of the very wide range of possible nucleic acid processing mechanisms that existed before the current forms of cellular life really were established and took off. The eubacterial and archaebacterial models may have taken off with remnants of the rest winding up parasitizing them.
Rampant horizontal transfer of genes, especially early when cell identity might not have been so strong, makes all this very complicated.
There's a school of thought in origin of life research that autocatalytic metabolism was important, and another that replicating polymers were important. The former posits that metal-ion driven cyclical reactions like the citric acid cycle can take off and take over, and wind up producing lots of interesting chemical byproducts that can then capture it and become discrete self-replicating units. The latter points out that elongating polymers in membrane bubbles speed the growth and splitting of these bubbles. They're both probably important. It should be noted too that these ideas intersect – one of the popular metabolic ideas, polyphosphate, is actually represented in our nucleic acids. Polyphosphate is an interesting substance that can be built up by the right chemial reactions, and can drive other ones when it breaks down. Every ATP, GTP, etc is a nice chemical handle on the end of a chain of three phosphates – a short polyphosphate. By breaking down those polyphosphates you build polymers.
Proteins obviously came very early and gave a huge advantage, and the genetic code is damn near universal with all deviations from the standard one obvioulsy coming in after the fact. Whatever could make proteins probably took over quickly. The initial frenzy, whatever it was, probably eventually lead to a diverse population of compartments processing their nucleic acids in diverse ways and sending pieces of their codes back and forth, which eventually gained advantages by building their own membranes, and eventually cell walls, in different ways. Some of these populations probably took off like mad, making the eubacteria and archaebacteria, and others remained only as horizontally transferred elements like viruses or transposons or the like.
Written in a hurry, may be edited or clarified/extended later.
Our sun appears to be a typical star: unremarkable in age, composition, galactic orbit, or even in its possession of many planets. Billions of other stars in the milky way have similar general parameters and orbits that place them in the galactic habitable zone. Extrapolations of recent expolanet surveys reveal that most stars have planets, removing yet another potential unique dimension for a great filter in the past.
According to Google, there are 20 billion earth like planets in the Galaxy.
A paradox indicates a flaw in our reasoning or our knowledge, which upon resolution, may cause some large update in our beliefs.
Ideally we could resolve this through massive multiscale monte carlo computer simulations to approximate Solonomoff Induction on our current observational data. If we survive and create superintelligence, we will probably do just that.
In the meantime, we are limited to constrained simulations, fermi estimates, and other shortcuts to approximate the ideal bayesian inference.
The Past
While there is still obvious uncertainty concerning the likelihood of the series of transitions along the path from the formation of an earth-like planet around a sol-like star up to an early tech civilization, the general direction of the recent evidence flow favours a strong Mediocrity Principle.
Here are a few highlight developments from the last few decades relating to an early filter:
The Future(s)
When modelling the future development of civilization, we must recognize that the future is a vast cloud of uncertainty compared to the past. The best approach is to focus on the most key general features of future postbiological civilizations, categorize the full space of models, and then update on our observations to determine what ranges of the parameter space are excluded and which regions remain open.
An abridged taxonomy of future civilization trajectories :
Collapse/Extinction:
Civilization is wiped out due to an existential catastrophe that sterilizes the planet sufficient enough to kill most large multicellular organisms, essentially resetting the evolutionary clock by a billion years. Given the potential dangers of nanotech/AI/nuclear weapons - and then aliens, I believe this possibility is significant - ie in the 1% to 50% range.
Biological/Mixed Civilization:
This is the old-skool sci-fi scenario. Humans or our biological descendants expand into space. AI is developed but limited to human intelligence, like CP30. No or limited uploading.
This leads eventually to slow colonization, terraforming, perhaps eventually dyson spheres etc.
This scenario is almost not worth mentioning: prior < 1%. Unfortunately SETI in current form is till predicated on a world model that assigns a high prior to these futures.
PostBiological Warm-tech AI Civilization:
This is Kurzweil/Moravec's sci-fi scenario. Humans become postbiological, merging with AI through uploading. We become a computational civilization that then spreads out some fraction of the speed of light to turn the galaxy into computronium. This particular scenario is based on the assumption that energy is a key constraint, and that civilizations are essentially stellavores which harvest the energy of stars.
One of the very few reasonable assumptions we can make about any superintelligent postbiological civilization is that higher intelligence involves increased computational efficiency. Advanced civs will upgrade into physical configurations that maximize computation capabilities given the local resources.
Thus to understand the physical form of future civs, we need to understand the physical limits of computation.
One key constraint is the Landauer Limit, which states that the erasure (or cloning) of one bit of information requires a minimum of kTln2 joules. At room temperature (293 K), this corresponds to a minimum of 0.017 eV to erase one bit. Minimum is however the keyword here, as according to the principle, the probability of the erasure succeeding is only 50% at the limit. Reliable erasure requires some multiple of the minimal expenditure - a reasonable estimate being about 100kT or 1eV as the minimum for bit erasures at today's levels of reliability.
Now, the second key consideration is that Landauer's Limit does not include the cost of interconnect, which is already now dominating the energy cost in modern computing. Just moving bits around dissipates energy.
Moore's Law is approaching its asymptotic end in a decade or so due to these hard physical energy constraints and the related miniaturization limits.
I assign a prior to the warm-tech scenario that is about the same as my estimate of the probability that the more advanced cold-tech (reversible quantum computing, described next) is impossible: < 10%.
From Warm-tech to Cold-tech
There is a way forward to vastly increased energy efficiency, but it requires reversible computing (to increase the ratio of computations per bit erasures), and full superconducting to reduce the interconnect loss down to near zero.
The path to enormously more powerful computational systems necessarily involves transitioning to very low temperatures, and the lower the better, for several key reasons:
Assuming large scale quantum computing is possible, then the ultimate computer is thus a reversible massively entangled quantum device operating at absolute zero. Unfortunately, such a device would be delicate to a degree that is hard to imagine - even a single misplaced high energy particle could cause enormous damage.
Stellar Escape Trajectories
The Great Game
If two civs both discover each other's locations around the same time, then MAD (mutually assured destruction) dynamics takeover and cooperation has stronger benefits. The vast distances involve suggest that one sided discoveries are more likely.
Spheres of Influence
Conditioning on our Observational Data
Observational Selection Effects
All advanced civs will have strong instrumental reasons to employ deep simulations to understand and model developmental trajectories for the galaxy as a whole and for civilizations in particular. A very likely consequence is the production of large numbers of simulated conscious observers, ala the Simulation Argument. Universes with the more advanced low temperature reversible/quantum computing civilizations will tend to produce many more simulated observer moments and are thus intrinsically more likely than one would otherwise expect - perhaps massively so.
Rogue Planets
Although the error range is still large, it appears that free floating planets outnumber planets bound to stars, and perhaps by a rather large margin.
Assuming the galaxy is colonized: It could be that rogue planets form naturally outside of stars and then are colonized. It could be they form around stars and then are ejected naturally (and colonized). Artificial ejection - even if true - may be a rare event. Or not. But at least a few of these options could potentially be differentiated with future observations - for example if we find an interesting discrepancy in the rogue planet distribution predicted by simulations (which obviously do not yet include aliens!) and actual observations.
Also: if rogue planets outnumber stars by a large margin, then it follows that rogue planet flybys are more common in proportion.
Conclusion
SETI to date allows us to exclude some regions of the parameter space for alien civs, but the regions excluded correspond to low prior probability models anyway, based on the postbiological perspective on the future of life. The most interesting regions of the parameter space probably involve advanced stealthy aliens in the form of small compact cold objects floating in the interstellar medium.
The upcoming WFIST telescope should shed more light on dark matter and enhance our microlensing detection abilities significantly. Sadly, it's planned launch date isn't until 2024. Space development is slow.