Is there a minimum altitude for ejection seats?
It depends on the ejection seat.

Modern zero-zero ejection seats are designed to be usable at zero speed, zero altitude.

Older ejection seats had different minimums which varied from model to model.

On a side note, the early F-104 ejection seats required quite a bit of altitude to deploy properly, since the pilot exited through the bottom of the aircraft. This was done because there was some concern that the pilot would hit the F-104's T-tail with a standard ejection seat.

EDIT

It appears that it may actually be possible to eject from an inverted aircraft. According to Wikipedia (bold added for emphasis):


  The minimal ejection altitude for ACES II seat in inverted flight is
  about 140 feet (43 m) above ground level at 150 KIAS. While the
  Russian counterpart - K-36DM has the minimal ejection altitude from
  inverted flight of 100 feet (30 m) AGL. When an aircraft is equipped
  with the Zvezda K-36DM ejection seat and the pilot is wearing the
  КО-15 protective gear, he is able to eject at airspeeds from 0 to
  1,400 kilometres per hour (870 mph) and altitudes of 0 to 25 km (16 mi
  or about 82,000 ft). The K-36DM ejection seat features drag chutes and
  a small shield that rises between the pilot's legs to deflect air
  around the pilot.