I began the Alphabet Points tournament series with a clocked tournament and switched to unclocked after the first one. Now, let's say right away that these events are fifteen-board, one board per round individuals, using SAYC only, so my experience may be different from other tourney formats.
During that first tournament I was deluged with requests to extend the time, claims that players were playing slowly, and on and on. Most of these would come with less than 2 minutes left in the round. I would arrive at the table knowing that one or two other tables had the same complaint, and of course it would be too late to determine anything. From the complaints I got the impression that many, many boards were not being completed, but when I checked the results I discovered that almost all of the top twenty had in fact completed all 15 boards on time.
I decided to switch to unclocked (actually a sort of 'unclocked but clocked' format) for the second tournament, and there are advantages...
--the tournament always is virtually finished in 120 minutes, because I added a rule that penalizes players 1 IMP or 1% per extra minute used. (Of course, the software cannot do this, but the lure of AlphaPoints allows you to tinker with the final results, for slow players or misbehavior, before you post the updated leaderboards.)
--Far fewer complaints about slow play. The only ones I get now are from people who have forgotten it is clocked, or from players who want to finish as quickly as possible, and I mollify them by pointing out that they are already way ahead of the field.
--Nobody ever loses a board to the clock, and nobody can ever delay to turn a zero into an average minus. Occasionally I will hear a delaying complaint, make an announcement to the tournament that you cannot lose a board to the clock, and then go to the complaining table and the problem is mysteriously solved.

--I have not done a study on this, but in entering the results into the AlphaPoints spreadsheet I get the impression that the slower tables produce a much higher proportion of the winners. I'm not seeing as strong an impression in the recent tounnaments, since the warnings/bans to tourney quitters and my recent decision to bar kibitzers until all players have completed 12 boards.
...and disadvantages:
--there are always complaints about waiting times, as the software requires at least three tables to be finished a board before shuffling the 12 or 16 players for the next round. In the late rounds this sometimes means a delay of five or more minutes.
--the 20-30 tables gradually divide into groups of players of similar speed, and after the division is set about 7-10 boards in, these groups play among themselves for the most part. Often a player will play with or against the same partner/opponent two or three times.
--The fastest tables are often done 30-45 minutes before the slowest. Fastest often simply means you were lucky enough to encounter nobody with connection problems, nobody who refuses to claim, and nobody who goes off to the bathroom for five minutes while waiting for a seat change that takes place one minute later.
The 'unclocked but clocked' rule is: if you don't reach board 15 after two hours, or finish it in ten minutes or less, you get penalized for extra time used. Frequent announcements of where everyone should be keeps most people on time, and during the final few rounds I keep a close watch on the 3-4 tables in the slowest group to make sure that they don't encounter any difficulties, advise a time-saving claim, warn them that they'll need to make up time in the next round(s) etc. Recently I have been watching close enough to assign conditional penalties to the players at the last table to complete each of the last 3-5 boards, which protects the unfortunates who get drawn into the slow groups at the beginning and are at their mercy. Usually these conditional penalties are discardrd when everyone finishes in time. Another thing I have done which helps a great deal is I have moved my announcements to the middle of the first round, after I deal with sitouts and subs.
I think this sort of thing may be the answer to the clocked/unclocked dilemma. Certainly the unclocked tournaments I play in take far longer than the advertised clock time, where Alphabet Points tourneys are never more than ten minutes over. My 'unclocked but clocked' format seems to have stopped the players who go overtime while still allowing the fast and lucky ones to finish in 70% of the total clock time. I think this might be a far-future wish-list item. The system could:
--penalize late finishers 1 IMP or 1% per extra minute used.
--inform players who are in the last 'group' that they must finish this round on clock time or they will get additional penalties added if they are also late finishing the event.
--a second onscreen clock telling players how many minutes left in the event.
--since most of the problems begin with round one difficulties, an option to hold round two until round one completed at all tables might help