Super Metroid, IMHO, is the best Metroid title. Those who grew up in that era of gaming will remember how epic of a title that was upon release...and how much of a staple it remains today!
I really loved Metroid Zero Mission. I kind of enjoyed Other M, although the story really undermined her character and made her more...feminine, which made Samus seem not badass in that game.
I really, really enjoyed Zero Mission; I remember getting it not too long after it was released. There was this "golden era" between the GBA (and its various incarnations) and the new generation on consoles, where Nintendo was just pumping out classic handheld titles; this was definitely one of them.
Noto nly was my first metroid game that I've played, but it was simply bu the mere fact that the game is almost perfect. I could tell so many things about that game taht just go so well altogether and I owuld never stop, that game is just amazing and really put Retro out there to send even more great games for us.
Most metroid fans would go for Super Metroid, but I really think that Prime takes the cake, it's atmosphere and immersion are just truly amazing, you really feel like you're Samus in that game and that you're going head first into the battle to stop the creation of Metroids. Amazing soundtrack, tight controls, and best of all, it tried out a new genre for the series that it really worked well with it, making 3 incredible games.