In Japanese title matches a unique time system is used.
Each player is alloted a fixed amount of time for the game. The amounts vary depending upon the match. Two day matches, the Kisei for example, allocate 8 hours of play to each person. A timekeeper is responsible for keeping the time and maintaining the time sheet.
Each time a stone is played, the timekeeper notes the time taken since the last play. If less than one minute of time has elapsed, the player is not billed for the time used. If at least one minute of time has passed, the timekeeper rounds the value down to the nearest minute and records the time used.
Once the time remaining for a player reaches a pre-stated amount, typically 10 minutes remaining in an 8 hour time allotment, the timekeeper will begin counting the seconds (byoyomi in Japanese). The count is done in units of 10 seconds, beginning with 10 and moving upwards (10, 20, etc). Once the player plays, the elapsed time is noted. As before the byoyomi, if less than a minute of time has passed, the player is not assessed for the time elapsed. If at least one minute has passed, the player is assessed the time rounded down to the nearest minute. If the timekeeper counts out all the remaining time before  the player moves, that player loses the game on time.
If a player goes down to the wire but always plays a move in time, he will always be shown as using (e.g.) 7h 59 - or 8.00 if he loses on time. But the actual time he spends can be 2 or 3 hours above that - there are players who go into byoyomi in the early fuseki, and there's no way to show that on the timesheet. It can be partly inferred from the actual finishing time.
Lunch: they will break off promptly at the designated time (e.g. 12 if they start at 8.30) and take one hour away from the board, no sealed move. Of course the hour does not count against anyone's time allowance. In the evening they will play on to a finish, or if it's Day 1 of a 2-day game, till the first move is made after the designated finishing time (e.g. 5 pm), but obviously this move is sealed.
Loo breaks and so on are in your own time, but everyone is much more accommodating and gentlemanly about this than in the chess world, and it has been observed that it can take 15 seconds to count out 10 seconds, etc etc.
The time sheet is more difficult to describe, but basically it's a repeating table, each part split into four rows. The top row has the move number in each cell (1-20, then 21-40 etc. up to 100 - if you need more, you get a second page and start again at 1-20).
Cells are empty in the other three rows. The second row is labelled "Time", the third "Clock", and the fourth "Total". When a player makes a move, and if he spends at least one minute on it, the timekeeper makes an entry in the second row (Time), showing the number of whole minutes elapsed, rounding all seconds down.
In the third row (Clock) he puts the number the minute hand  points to. He will have already written in the margin the time when the game started (e.g. "Started at 8.30" -- so if the first move took 4 minutes, he will write 4 in row two and 34 in row three.
In row four (Total) he writes the total elapsed for each player by adding up the respective figures in row two. In the first hour he just writes the minutes. After the first hour he writes the total out fully (e.g. 1.25).
If a player makes a move in less than a minute, a "/" is put in row three (Clock), but rows two and four are left blank. In other words, nothing is counted against his time allowance.
That's it for the ENTIRE game, really. It's a mistake to think of byoyomi as overtime. If a player exceeds his alloted time, he loses. The only difference byoyomi makes is that in the last 10 or 5 minutes, as a courtesy, the timekeeper will count out the seconds (and he will mark the clock time in row three in brackets to remind himself to count). The way he does the counting can vary. The timekeeper will often ask each pro how he wants the counting to be done. Typically a pro might then say: "just speak once when I reach the last five seconds except in the last minute, then I'd like you to speak at 30 seconds, 40 seconds, and then count out the last ten. (Byou-yomi means counting off the seconds, not reading). Many pros are happy with plain vanilla, of course, and will accept a regular style of counting like the one Richard mentions.
Since we are on time limits, you might like to know that the longest game on record was 240 hours (no time limits). The longest with time limits was 40 hours each: 46 hours combined were used. 
Richard Hunter: First of all, a big thank you
to John for his prompt response and
detailed account about.
I found it very interesting. I wrote an article called [Byoyomi Explained| http://www.britgo.org/bgj/10643.html] a few years ago and didn't want to repeat myself too much. At my request, Steve Bailey has kindly posted it on the BGA web site.
It ends with an anecdote about loo breaks, perhaps slightly different from John's comment. I remember that they discussed differences between go and shogi in this respect on the Igo/Shogi news program one time.
This system is basically Japonese Byoyomi (as used on go servers) without main time but with several hundred periods.
Can someone elaborate on the history of the time system described here? When it was first used? where? etc.
 For logical reasons IMHO it should be
If the player does not move before the
timekeeper counts out all the remaining time, that player loses the game on time. With other words, and academic OC, if time runs out at the very same moment the turn ends, the player hasn't made it and loses on time.
 Which clock is meant, the normal one for everybody?