Did they pull them out or did they just suffer with them?
If I may, I would tackle this question first from a slightly different angle, that of painkillers and anaesthetics.
Since antiquity people have employed herbal anaelgesics inclding very careful doses of Hemlock as a sedative (Keller 2005). While surgery without anaesthesia was incredibly common in the past, there are anaelgesics and sedatives from the 9th and 10th century based on the use of hemlock, Opium, Mandrake and Henbane soaked into a sponge of all things. Thus inhaled, the patient would fall asleep whereupon the surgeon could get about their business (Keller 2005, Prioreshci 2003).
Opium itself was used by the Romans, though not as standard for surgery until the middle ages according to Keller (2005).
As one might imagine proper dosage control and fatal overdose where rather a bother unless you had a physician aware of this risk and had a way of accounting for this risk, due to lack of standardised practice (Keller 2005).
So, to return to dentistry, certainly it was possible to dose the ever loving crap out of a patient and go to town on the tooth.
Actually tackling a painful tooth coming in or a rotten one has been done for almost 10,000 years, with drilled molar crowns being found in Pakistan between 7,500 and 9,000 years ago (Coppa et al 2005). More specific to the middle ages however, treatments included removal, use of anaelgesic amulets, bloodletting, and probably the most effective: herbal painkillers (Anderson 2004). Anderson does howeve say survey of documentation from the 12th and 14th centuries primarily regards non-invasive treatments as preferable (2004).
So all in all you're probably looking at rudimentary herbal painkillers. The paper by Anderson is probably the best thing to look into for further detail on those treatments, while Keller gives a decent survey of just the sedatives and painkillers.
Prioreschi, P, 2003, Medieval Anesthesia-the spongia somnifera, Medical Hypotheses, 61(2):213-219.
Edit: quick change to referencing format cock up
I'd like to tack on a follow-up question. How dangerous were dental infections in the same time period?
Were they commonly fatal, or did they pull the teeth themselves and hope for a clean recovery?
As a follow up question. Did wisdom teeth cause a problem? Are teeth today larger due to better nutrition? Did peolle loose teeth quicker? Maybe there was always room for the wisdom teeth due to tooth loss?