The first game system I remember thinking "Wow, this is a good system" was R. Talsorians Interlok system. It was clean and crisp and ultimately deadly to characters who went guns blazing into whatever encounter was on the table. Interlok was used in a variety of games. From Cyberpunk & Cybergeneration to Mekton and Bubblegum Crisis and was later revamped and tooled with the old Hero system to give us Fuzion.
d10 + Skill + Stat +Modifier vs d10 + Skill + Stat + Modifier
How simple is that?
In between then and now there were a ton of systems we played with. There was BRP (Basic Role Playing), Chaosiums In House system mainly used for their flagship Call of Cthulhu, but also used for Stormbringer and the newer Laundry files RPG. I've always like BRP for its ease of use and 1-100 mechanic.
I wasn't a huge fan of Dice Pool systems like White Wolfs series of games Vampire, Mage, Wraith and Werewolf that used a crapton of d10s or even Shadowrun and it's insatiable need for millions of d6s. It worked smoothly, but I hated having to carry around more than a set of dice.
it might slow some people down but sometimes I like the crunchy stuff. Don't get me wrong, simplicity has a place but sometimes I need some numbers to make me feel that something has been accomplished. The crunchiest thing I own these days outside of Pathfinder is Eclipse Phase which is based loosely on the same d100 mechanic as BRP.
As of this writing though I have to tell you I've really grown to love the Apocalypse Engine system, notably Apocalypse World and more noticeably Dungeon World. It gives me the classic feel of OSR with the added storytelling elements that I've grown to like from some modern game systems.
In the end, I don't think I have a favorite system of all time. I like a variety of systems for use in different kinds of games. New systems are always coming out so I'm sure that a new game will come out that I will rave on at a later time.