The combo that has worked the best for me as Meta Knight is the U-Air/Up-B combo. It's extremely simple, but like I said, it works. Against almost any character at almost any percentage, you can string together a fair amount of U-airs and finish the combo with an Up-B. The Up-B will normally kill at 100-130% (minimum), and the preceding U-air's will normally bring your opponent to around that percentage (that is of course depending on the percentage your opponent is at when you start the combo). If not the Up-B will normally launch your opponent far enough to execute an effective edge-guard.
That's normally a very easy combo to start-up as well. You can lead into the combo very well with an U-Smash or U-Tilt . You can also D-Throw/Dash A/U-Tilt/U-Air/Up-B as well if your opponent's at a lower percentage or if you just want a flashier combo. It's less reliable though.
I've also noticed that Meta's Up-B is probably his best killing move, and that it's not used very often as such. I haven't seen one person who uses that move for killing. Granted, I haven't seen a whole lot of people play Meta Knight, but I digress. Like I said, it's very easy to combo into and will kill at relatively low percentages, though the move is also virtually un-punishable, it has almost zero overall lag, a fairly large hitbox, and it can be used out of a shield. His D-Smash is probably the next most reliable KO move, and I've found that it's a lot more situational than his Up-B. What I mean by that is that the D-Smash can only be used in a handful of situations, whereas the Up-B cannot only be used in more situations, but you can create more situations in which you'll be able to land that attack by comboing or even shielding at the right time. You can also wall-spike your opponent against the side of a stage under the right circumstances if he/she tries to edge-guard you while you're recovering.
And just one more note, and I think this was mentioned by Gimpyfish or someone else in one of his videos somewhere, is that Meta Knight can also apply some of the best shield pressure in the game. You can very often just poke at your opponent's shield with a D-Tilt or F-Tilt, and because Meta's attacks possess very little lag in general, the tactic is hard to punish.