The PC(USA) is now on the brink of sliding under 2M, down from their peak of 4.3+ million (when the UPCUSA) in 1967.
The PCA is closing in on 350,000
The EPC has, I think, about 80,000
The OPC and ARP are each somewhere past 30,000 [correct me here as needed!]
From there it drops precipitously. I can't think of any in the 10-25,000 range at present.
The RPCNA has about 6,000 and the BPC has maybe 3,000 members.
Below that is the potential realm of the micro-denominations. So I would first want to define a micro-denomination as something below those last numbers--well below. So here consider the total membership and the number of churches.
But something else might also factor in, namely, that the group would be the result of one or more schisms. Most, if not all, of these groups are consciously doctrinal, with studied convictions. Consequently, many of the small groups have rarified or even unique doctrines or convictions which prevent them from merger with other groups that are otherwise of like mind. Ask yourself why don't all of the exclusive psalmody groups merge together? (Q.: aren't most of the micro groups EP?) A joining and receiving with the RPCNA would probably be the most profitable and least troublesome. But it doesn't happen.
That last consideration in turn reveals another likely distinguishing character of a micro-denomination, namely a single leading figure who more or less controls the whole group. To merge with others would diminish the power or control enjoyed. In some cases that power might be cultic or tyrannical, but often it is well-meaning and merely leveraged to keep things on the straight and narrow.
So, in sum:
1. Fewer than 2,000 members
2. Fewer than 50 churches
[if all of the churches in the group have fewer than 100 members, that might be another defining factor]
3. Doctrinal precision to the point of excluding merger with similar groups
4. A single dominant leader who may exert autocratic, cultic or even tyrannical leadership
5. Ben's note of vintage is good, but by itself not determinative. The Reformed Presbyterian Church, General Synod got down to 9 churches in the early 20th century. I would call that a micro-denom. at that point, just on the basis of size. But they built back up to about 28 churches by the time they merged with the larger portion of the BPC split to form the RPCES.