Yes, if you got married once your husband was already in the US, you can go ahead and file for his permanent residence on the basis of marriage to a US citizen.  It really depends on how soon after his entry you got married so as not to have it look like misrepresentation of intent at the time of entry.  Once you file for adjustment of status, he will be in that "pending AOS applicant" status until the interview and adjudication of his application so even if the 3 month I-94W is expired, he can remain in the US pending the outcome of his application.  If you married very soon after his entry, you may want to think about the reasons you will want to provide to the USCIS at the time of the interview as to why you did that and not gone the traditional route of petitioning for him while he was still overseas.  There are many people who do get married while on the visa waiver and then successfully file for adjustment of status.  However, it is best done when the marriage takes place almost at the end of the 90 day window granted on the I-94W and not at the beginning.