I suspect the problem is in the way you're trying to use your timer class: it seems more or less fine; though I was a little confused as to where your isDone() method gets called from.  You can actually do all the work in the work() method.  I've tweaked your code and simplified it a little; though I think there's still room for improvement:

1. Timer t;
2. void setup() {
3.   t = new Timer(10);
4.   t.start();
5. }
6. void draw() {
7.   if(!t.work()){
8.     println(t.elapsed);
9.   }
10.   else {
11.     println("finished");
12.     // trigger the next timer...
13.   }
14. }
15. /* Very basic timer class
16.  takes one parameter, max. time in sec.
17.  remember to make it run on main loop!
18.  */
19. class Timer{
20.   /* separate your class properties onto separate lines: makes it easier to read.
21.      Also it's clear these are related to time, so there's no need to tag the word 'time' onto
22.      your variable names: this also makes it easier to read ;)
23.   */
24.   int elapsed; // changed this before I decided to remove time from the variable names
25.   int start;
26.   // int current; // no real need for a 'current' time variable
    
27.   int limit;
28.   Boolean running;
29.   Timer(int limit)  {
30.     this.limit = limit;
31.     // no need to call stop().  Booleans default to false ;)
32.   }
33.   void reset()  {
34.     start = millis()/1000;
35.     // not much point doing this calculation: it's always 0
36.     //elapsed = current - start;
37.     elapsed = 0;
38.   }
39.   void start()  {
40.     running = true;
41.   }
42.   void stop()  {
43.     running = false;
44.   }
45.   Boolean work()  {
46.     if(running) {
47.       elapsed = (millis()/1000) - start;
48.     }
49.     if(elapsed >= limit) {
50.       stop(); // no point letting it carry on...
51.       return true;
52.     }
53.     else {
54.       return false;
55.     }
56.   }
57.  
58. }
59. void keyPressed() {
60.   t.reset();
61. }

Ignore changes to coding style (e.g. I removed new-lines from before opening braces) as that's a matter of taste (or in my case OCD ); but the points about variable names and their presentation stands: when writing classes you need to consider the possibility that other people will have to work with them; so make their lives as easy as possible.  Good to get into the habit from the start ;)

This might help you figure out how to apply it to your use case...

That was of great help, thanks! (and thanks for the writing tips - I'm such a mess!

OK - I admit I didn't test it all that thoroughly

Anyway - a couple of problems.  First: you obviously need to set 'start' to the current time when the timer starts - i,e, call reset(0 from start(); otherwise it'll be past the limit as soon as it starts.  Second problem - you only want to call start() once, to get it going.  If you call it every frame you'll keep resetting the timer to 0:

1. Timer t;
2. Timer t2;
3. boolean t2Started;
4. void setup() {
5.   t = new Timer(3);
6.   t.start();
7.   t2 = new Timer(4);
8.   t2.stop();
9. }
10. void draw() {
11.   if(!t.work()){
12.     println(t.elapsed);
13.   }
14.   else {
15.     println("finished");
16.    
17.     if(!t2Started){
18.       t2.start();
19.       t2Started = true;
20.     }
21.   }
22.   if(!t2.work()){
23.     println("t2 elapsed: " + t2.elapsed);
24.   }
25.   else {
26.     println("t2 finished!");
27.   }
28. }
29. void keyPressed() {
30.   t.reset();
31. }
32. /* Very basic timer class
33.  takes one parameter, max. time in sec.
34.  remember to make it run on main loop!
35.  */
36. class Timer{
37.   /* separate your class properties onto separate lines: makes it easier to read.
38.      Also it's clear these are related to time, so there's no need to tag the word 'time' onto
39.      your variable names: this also makes it easier to read ;)
40.   */
41.   int elapsed; // changed this before I decided to remove time from the variable names
42.   int start;
43.   // int current; // no real need for a 'current' time variable
44.   int limit;
45.   Boolean running;
46.  
47.   Timer(int limit)  {
48.     this.limit = limit;
49.     // no need to call stop().  Booleans default to false ;)
50.   }
51.  
52.   void reset()  {
53.     start = millis()/1000;
54.     // not much point doing this calculation: it's always 0
55.     //elapsed = current - start;
56.     elapsed = 0;
57.   }
58.  
59.   void start()  {
60.     reset();
61.     running = true;
62.   }
63.  
64.   void stop()  {
65.     running = false;
66.   }
67.  
68.   Boolean work()  {
69.     if(running) {
70.       elapsed = (millis()/1000) - start;
71.     }
72.     if(elapsed >= limit) {
73.       stop(); // no point letting it carry on...
74.       return true;
75.     }
76.     else {
77.       return false;
78.     }
79.   }
80.  
81. }

Though actually, instead of that extra external boolean you could probably just check that 'running' is false before calling reset() in start()...  (edit: don't count on that working though.  I'm tired and not thinking particularly straight. )

Great, thanks, now it works! Tired or not, it solves my issue and I've learnt new things, thanks!