I know, me too. I'm missing I think 7 episodes from Season #1, that I've never been able to catch anywhere in HD. I keep hoping they'll eventually run the series from start to finish in the evenings or something, like they used to run all the Stargates, they've got enough episodes under their belt and especially after this season to run them daily if they wanted too.
All the mini-marathons with the exception of the 22 hr one they ran a while back have seemed to all be season 3.5 over and over. I've got my DVR set to record any and all Eurekas.