How do I get a "Perfect" in Bit.Trip Runner?

There is a very easy way to guarantee you get a perfect score -- simply play on "PERFECT" difficulty. You automatically fail the level if you ever miss something that would contribute to a perfect score. Thus the levels become, simply

! = main level completed perfectly

!! = main level & retro warp level completed perfectly (So PERFECT score!!)

If you don't want to restart your save file and play through every level again, however, here's a general guide:

The trick to getting Perfect scores is simply a matter of getting all the gold, and performing all score increasing actions in a single run. In perhaps 90% of the cases, getting all of the gold will get you the perfect score, and there are only a few outliers where you have to make an effort beyond that of simply collecting the gold.

Here are the actions that score points:

• Kicking through a breakable object (Crystals, Stop signs, Boxes)
• Hitting a Springboard
• Bouncing off a Spring enemy.
• Reflecting a Bullet
• Picking up Gold
• Picking up a "+" object.

When given a diverging path with a choice (i.e., either hit a springboard or pick up a gold piece) always follow the gold and the "+" multiplyer, as these two objects are the biggest score boosts by an extremely wide margin.

When given a choice to either hit a points item or survive, chose the latter. Some points objects merely exist to present false choices - going after any item that will result in your immediate subsequent death is not required to score the perfect.

Quoted from the wikipedia article:

The perfect completion of a retro challenge will award players with an exclamation point beside the stage and the word "PERFECT" beside the score in the scoreboard, but only if they have done everything "extra" (i.e., jumping on top of springboards that they do not need to in order to finish) in the level beforehand.

Edit

According to this gamefaqs forum thread:

! = All golds collected; advanced to Retro level

!! = All golds collected in Retro level

As such, it sounds like you need to not only get all the golds in a zone, but also all the golds in its retro levels. A bit of forewarning, I don't actually own B.TR, so I can't confirm any of this data.