Metal Slug 3. It has the best use of the Neo color pallette of the entire series, along with probably the smoothest animation for the seemingly endless variety of critters to kill, and the humongous bosses. Not to mention its the most bang for your buck game in the series, with level 5 being almost an entire Metal Slug game in itself, taking about 20 minutes to complete.
Metal Slug the original, while being fantastic with its detail in the explosions and toilet humor, suffers from some bad control mechanics and a really weak color pallette. Most of the game is just different hues of Tan, Green and Brown. It still looks good, but the glaring difference between this and 3 is obvious.
I haven't had the pleasure of playing 2,X, or 4. MSX looks darn good though and I would consider paying the large sum this game commands for an AES cart of this.