Yes, rabbits get a lot of ear problems. Ear scratching and head shaking are usually signs of an inner ear infection or ear mites. The vet should be able to tell which of these it is. If it is ear mites, he will get an antiparasitic like Revolution, ivermectin, or Advantage (do not use Frontline on rabbits!). It is usually dosed on the skin, and will need a second dose 10-14 days after the first one. Of these, ivermectin is the most commonly available (you can buy it over the counter at farm stores), but some bunnies do not react well to it and can have life-threatening events.
If it is an inner ear infection, the vet should give you oral or injectible antibiotics. Many vets are reluctant to use strong antibiotics on rabbits, because some antibiotics (those of the -cillin family in particular) are toxic to rabbits if given orally. For this reason, they usually start with the weakest, least invasive antibiotic, which can delay treatment of the infection and allow it to spread or cause permanent damage. For instance, if your vet recommends an antibiotic ear drop, that's totally unacceptable for an inner ear infection. The reason is that it cannot penetrate deep into the inner ear if applied to the ear canal nearly as well. An example of this would be Baytril Otic.
Other drugs that vets like to give but that have very low effectivity in rabbits are sulfonamide drugs. This is the earliest class of antibiotics developed, and as a result, many many bacteria are resistant to this class of drugs. In addition, they can cause GI upset in rabbits as well. Anything that has "sulfa" in the name is likely to not be strong enough and have some GI complications.
The vet may want to start with enrofloxacin (Baytril) oral solution. This is a pretty broad-spectrum drug, but again many bacteria are resistant to it. It's the animal form of Cipro (ciprofloxacin), which you probably know is over-used in humans and has lost a lot of its potency because of that. It may work, but I wouldn't use it for more than 4 days without seeing improvement--that would indicate resistance to me.
Injectible antibiotics are going to work the best, usually. These include the -cillins (amoxicillin, penicillin) and Convenia (cefovecin). Other good ones that are orally administered are azithromyacin and cloramphenicol.
This is a list of rabbit-safe antibiotics:
Finally, she will need at least a 14 day supply as you have to continue dosing antibiotics for several days after the infection appears to have cleared up in order to make sure it is gone. It is also useful to add probiotics to the diet when the bunny's on antibiotics to keep their GI bacteria in order. Bene-Bac is made for dogs/cats or small animals and can be found at many big box pet stores. ProBios is also a probiotic with horse, sheep, goat, cow, and small animal formulations, available at many farm supply stores. These are only available in the US so if you're not in the US we'll have to recommend some other probiotics.
Hope this helps! It's more important for her to be seen by a rabbit-savvy vet for this condition than to have her seen tomorrow, so if you can only get her to an emergency vet tomorrow, I would wait until you can get a rabbit vet. We have extensive listings of rabbit-savvy vets on this site, from all over the world.