Space: 1999 has the following standout episodes, in my opinion:
Breakaway (the first story, very 2001-ish feel to the effects)
Black Sun (the "theological premise" behind the show, so to speak)
Another Time, Another Place (all around excellent story)
Guardian of Piri (Catherine Schell appears in this other-worldly story)
The Last Sunset (a personal favorite)
End of Eternity (creepy...)
Mission of the Darians (some cool concepts, Joan Collins)
Dragon's Domain (scared me as a kid...as it scared every other kid that watched it back then)
Year Two episodes vary in quality, and there are a handful of standouts, but I still stick with recommending Year One stories.
Watching Space: 1999 is a bit of a culture shock when it comes to Sci Fi. It's a show that usually has to grow on you. It's very stylized, visually stunning, and often unexplained and very "sterile." Once you see an episode or two, you will know what I mean
The above link to YouTube features 2 promos, one for Dragon's Domain, the other for End of Eternity. Both accurately reflect the "feel" of the shows.
Here's one of the more frightening sequences from Dragon's Domain: