I like elongated cents, and I don't know why... Especially since elongating a cent goes against so many coin collecting rules.

1) Coin collectors do whatever they reasonably can to preserve the condition of coins by protecting them from damage.  Coin elongators intentionally inflict severe damage to a coin.

2) Coin collectors are taught that cleaning a coin is a huge no-no, except for certain methods of professional conservation that are meant to prevent further deterioration of a coin exposed to damaging environmental contaminants.  Some coin elongators prefer to clean their coins before elongating them.

3) Coin collectors are taught to NEVER polish a coin, for ANY reason.  Some coin elongators take cleaning a step further and polish their coins, either before (usually) or after elongating them.

Elongating a coin effectively takes that coin out of its mintage population from a collecting standpoint.  Many times the date and mintmark are totally obliterated, so there's no way of proving the mintage anymore.  Even if the design, date, and mintmark are still discernable, people looking to add a certain year-and-mintmark cent to their US cent collection aren't looking for an elongated version.  Because of this, the thought of the numismatically-uninformed public randomly running cents through penny presses is enough to make the average numismatist a little nervous, for fear of a precious rarity being destroyed.  

Although it's possible, the odds of destroying a rarity are pretty small, especially as most cents still in circulation today are the overproduced modern copper-plated zinc versions, which make lousy elongates.*  Since it's a collector/numismatist who is more likely to know the older copper cents make better elongates,** it's a fair assumption that many of those people using older coins are searching them before deciding to elongate any.

What about cleaning them, though?  Should you?  Well, it's not like cleaning them is going to drastically reduce their collectible value as coins, because smashing them already does that; so that's of no consequence.  

There's an argument to be made that you *should* clean them (with something like an acetone bath).  By not cleaning them first, whatever surface contaminants the coin has will be smashed into it, possibly leading to deterioration of your elongate over time.  You could also say you are passing along contaminants to the elongate belonging to whoever uses the press next.  But because so many non-numismatists use these presses and don't know or care about that, you have to assume that is going to happen anyways.

Beyond removing contaminants, is there anything else to consider?  Only personal preference or "artistic effects."

Some types of cleaning do remove toning.  If what you want is a bright, shiny copper elongate with little trace of the original cent design in the background, you should remove the toning.  Swishing the cent in a solution of white vinegar and salt will usually do this very quickly, but could turn the copper a pinkish color if done too long.  If you really like shiny, take the extra step and polish it with a copper polish and soft rag.  Then it will really shine (this also helps turn the pinkish color back to copper).

Leaving the toning on a cent may give you an elongate with contrasts, as some of the toning may be removed as the press may bring fresh metal to the surface as the original surface is deformed.  Whether this is good or bad depends on what you want, and sometimes a little luck.  
If you leave toning on the coin, you may end up still seeing some of the original surface design in the background of your new elongate design.  This could be distracting, making it hard to see the new design.  Then again, it could yield some really cool results.  I pressed some toned wheat pennies at the National Museum of the US Air Force, and some came out with "LIBERTY" or "UNITED STATES OF AMERICA" or "IN GOD WE TRUST" in the background of a B-17 bomber and a P-51 Mustang.  You can't really control the orientation of the words with the elongate design, but you might get lucky and have things align in a neat way.  And if your coin has colorful toning, it can yield an interesting, colorful elongate.

By leaving toning on at least the obverse, you can possibly get one more benefit:  an elongate that still shows the year and mintmark of your cent.  This is easiest on a uniface elongate press, which only presses an image on one side, leaving the other side smooth and blank. On the Air Force Museum press, I figured out that by putting the cent into the coin slot with Mr. Lincoln facing right, the date and mintmark would be on the smooth back of the elongate, and usually very visible instead of lost in the elongate design.  That was especially fun when I chose a date that was significant to the elongate subject (like a 1942 cent for a B-17 bomber).

One more thing:  what about all those collectors trying to fill out a Whitman folder... aren't I destroying their chances of finding the coins they need?  Not really.  When I select cents to squish, I usually select those with scratches, dark spots, PVC damage, or other problems that would tend to make them undesirable.  I can then clean and polish them without guilt.  By doing this, I feel like I'm redeeming these "uncollectible" examples and giving them new life as a collectible elongated cent.

Leave it to a numismatist to complicate something as simple as putting coins in a machine and cranking the handle!  Think about what you want, and experiment.  You could turn out something even more interesting than a simple pressed penny.

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*(US cents changed their metal composition in mid-1982 from 97% copper to a zinc core plated in copper.  When you press a zinc cent, the silvery zinc shows through the copper where the design deforms the coin.  The zinc/copper contrast sometimes makes it hard to see the design, and in my opinion doesn't look as nice.)

**(This is also an assumption on my part, but also a fairly safe one I believe.)