Every Standard Model process except an extremely high energy and exotic theoretically possible process called a sphaleron, separately conserves baryon number (i.e. quarks minus anti-quarks divided by three), and lepton number (i.e. leptons minus anti-leptons). Even sphalerons conserve B-L.
But, the baryon number of the universe (essentially equal to the combined number of protons and neutrons in the universe) is a high positive number since anti-matter baryons are extremely rare. The same is true of charged leptons which are almost exactly equal in number to the number of protons in the universe; positrons, anti-muons and anti-tau leptons are all extremely rare.
There are far more neutrinos in the universe than there are baryons and charged leptons combined. But, it isn't obvious what the ratio of neutrinos to anti-neutrinos is in the universe, although there are hints that the number of anti-neutrinos greatly exceed the number of neutrinos.
Even the number of anti-neutrinos measurably exceeds the number of neutrinos in the universe, the excess of anti-neutrinos over neutrinos creates a negative lepton number for the universe that swamps the total positive baryon number of the universe and the positive lepton number from charged baryons in the universe. Thus, B is a very large positive number, L is probably an even larger negative number, and B-L is a very large positive number.
Fundamental dark matter particles that were antimatter and had baryon number, or were matter and had lepton number, could help even the scales a bit. But, given the known total amount of dark matter in the universe and reasonable assumptions about the mass of dark matter particles, no fundamental dark matter particle with either of those properties could resolve the matter-antimatter asymmetry in the universe.
Careful analysis has determined that Standard Model sphaleron processes could not account for the current matter-antimatter asymmetries even over the entire history of the universe from a B=0, L-0, and B-L=0 initial condition which is often unquestioningly assumed at the initial moment of the Big Bang.
So, why does our universe have such a matter-antimatter imbalance for different classes of fundamental particles (i.e. B>>0, probably L<<0, and probably B-L>>0)?
There are basically four possible solutions:
(1) The Universe Did Not Begin As Pure Energy. The starting point of the universe is not B=0, L=0 and B-L=0. Instead, the universe started with B>>0, L<<0 and B-L>>0 and has preserved those numbers ever since. They are arbitrary laws of the universe just like other physical constants in the Standard Model and General Relativity like the speed of light, or Planck's constant.
(2) We Can't Observe Important Balancing Parts Of The Universe. The universe includes places we cannot see due to General Relativistic singularities and balancing baryons and leptons to create B=0, L=0, B-L=0 are on the other side of singularities between us in the observable universe and the relevant event horizons. This has two subcomponents:
(a) Before The Big Bang. There was one anti-baryon created for every baryon, but the anti-baryons are overwhelmingly located before the Big Bang and are moving backward in time. Likewise, leptons and/or anti-leptons necessary to balance lepton number are overwhelmingly located before the Big Bang. Antimatter moving forward in time towards the Big Bang, and matter moving backward in time towards the Big Bang fuel this massive energetic event which created particle-antiparticle pairs in large numbers which unequally sorted antimatter particles "before" and matter particles "after". This is very similar in principle to possibility (1).
(b) Inside Black Holes. Anti-baryons, positrons, anti-muons, anti-tau leptons, and ordinary neutrinos are disproportionately sucked into black holes relative to baryons, charged leptons, and anti-neutrinos. This sorting could arise from general relativity acting on pair production at the event horizon, or could arise from some other process. For example, if black holes tend to have negative electric charge, they will tend to suck up anti-protons in preference to protons. One fruitful way to investigate this possibility would be to look at the relative matter-antimatter composition of Hawking radiation.
[UPDATE June 16, 2014:] Given that the black hole at the center of the Milky Way galaxy has a strong magnetic field, and appears to be quite typical of black holes at the center of ordinary galaxies, the possibility that black holes are usually charged in a way that biases what does and does not enter a black hole based upon its electric charge which is correlated strongly with matter-antimatter character, is worth taking seriously. [End UPDATE.]
(3) The Dark Sector Balances The Books. There are particles in the dark sector (i.e. those that account for dark matter and dark energy phenomena) that have baryon number and lepton number that balance out the matter-antimatter imbalance in observed matter. Note that for the dark sector to contain the correct number of anti-baryons and leptons, and for the total mass of dark matter particles to coincide with the measured value, it is probably necessary for dark matter to be made out of composite particles rather than fundamental particles if the mass of each dark matter particle is in line with estimates inferred from astronomy observations.
The inferences one draws in general about the dark sector, if it is to resolve these imbalances (or at least to bring B-L to zero) provide an interesting exercise that depending on the neutrino-antineutrino ratio may imply composite dark matter, dark matter dominated by heavy dark matter particles with a wealth of very light (perhaps neutrino or axion mass scale) particles that have only a minimal effect on cosmic structure because they are so light relative to other kinds of matter in the univese, or even a dark sector in which dark matter phenomena are primarily a function of modified gravity laws rather than dark matter particles (if the neutrino-antineutrino ratio is only every so slightly balanced in favor of antineutrinos, leading to L=0 or L=-B).
(4) Beyond The Standard Model Processes Do Not Conserve B and L and B-L. There are additional new physics processes beyond the Standard Model that violate baryon number conservation and lepton number conservation in ways that are almost impossible to observe now, but would have led to baryogenesis and leptogenesis in the highly energetic very early universe immediately after the Big Bang.
This is the predominant view among theoretical physicists, but this really shortchanges equally plausible options (1), (2)(a), (2)(b), and (3) without a good reason for doing so.
I would note that Option 2(a) is a particularly elegant solution that is also parsimonious, and could be supplemented in part by 2(b) and (3) to some extent that would not have to be complete.
It would also be an interesting exercise to determine the total mass-energy of the universe and compare it to the total number of particles in the universe and the total B+L of the universe.