“[Punctuation] is a large subject. Whole books have been written about it, and it is still true [...] that no two authorities completely agree.”
Sir Ernest Gowers (“The Complete Plain Words”)

American Punctuation
The main problem with today’s American punctuation is the fact that it is solely based on speech rhythm. Correct punctuation has little to do with that; its foundation should be the sentence structure (main clause, subordinate clause, apposition etc.). One can’t turn the wheel of time back and strictly apply this principle today anymore; it’s just too tough for hoi polloi. One can, however, strive for more perfection: As a guideline one can say that the best comma is a comma that is both syntactic and rhythmic. Syntactic commas are always right but need not always be put. The worst commas are the purely rhythmic ones. These are the commas ignorant American (and German) writers have a predilection for. In addition one can say that a sparing use of commas is a good idea. A wrong comma speaks volumes; a missing one can always be attributed to negligence.

Right
“I love parties”, he said.
She called me a “freak”.
He said: “Yes.”
... dogs, cats and sheep etc.

Wrong
“I love parties,” he said.
She called me a “freak.”
He said: “Yes”.
...dogs, cats, and sheep, etc..

The last of the above examples is especially important I think: the ellipsis used wrongly. No space before (or after) the ellipsis means a word is short of a component (below: “phagocyte”); a space between the word and the ellipsis means that a sentence is incomplete:
Words beginning with “phago...” always have ...

An equally big problem is the use of periods and commas in combination with inverted commas.
This example is from Macworld, July 1999 (p. 17): I enjoyed visiting the sites described in the “Web Traveler’s Companion.”
This makes one shudder! It is simply unbelievable that the feel for syntactic units has gotten lost to such an extent in American grammar. The period in the above example clearly refers to the whole sentence, not to the quotation marks stuff, and therefore its only place is outside of the final inverted commas. For a European reader this is perfectly obvious; even school kids have no problem with this principle.
The leading American grammarians, however, refuse to acknowledge it and continue to propagandize their absurd, illogical and primitive punctuation rules.
With such rules you will ruin any book, any document, any software’s user interface.

Another very bad habit is the way captions and headers are treated in American and British English. Basically the rule is to capitalize captions, and that is a good idea. But nobody gives a damn about this rule! What one usually sees is a strange mixture of uppercase and lowercase words. “Important” words are capitalized, the rest not. I think English captions should be consistently capitalized.
In hand written texts one sees even crazier things: Majuscule ‘R’s are used within a word! Right beside lower case ‘r’s ...
Needless to say that capitalizing certain words within a sentence is also a sign of bad taste. Apart from proper names nothing should be uppercased within a sentence.
The latest trend: Inverted commas are no longer inverted commas but a combination of a grave (!) and an inverted comma (`example'). This of course is crazy and totally unacceptable.

Syllabification is another very serious problem in American texts. Instead of following the rules of logic, word history and morphology, American grammarians – much like in the case of inverted commas plus periods – have decreed a primitive “one rule for everything”-approach. This leads to absolutely grotesque things like “typog-raphy” (Macworld, 7/2002, p. 84) that simply ignore the components of a word and treat it as if it were just a sequence of characters.
The above, mind you, isn’t an erratum! The American Heritage Dictionary approves of such barbaric syllabification!