My three, just off the top of my head, would be:
Harry's Game by Clannad
Beautiful, haunting, sad, it was so perfect for a series set at the height of The Troubles in Northern Ireland
Battlestar Galactica (Re-inagined 2004 version) by Bear McCreary
Gorgeous and original, this music did everything a TV theme needs to do while sounding utterly unlike anything else.
They did a fabulous live concert of music from the series, full video here:
https://www.youtube.com/watch?v=Y3yovHB-drE (the actual title theme starts at about 13:40)
Space 1999, BUT.... (and here's a way to start a geek-fight on the internet...
)
Series 1 (Barry Gray) or Series 2 (Derek Wadsworth?)?
I say Series 1 hands down, but other opinions are available....