kari,
For slow counter & timer (< 1 Khz) software counting is the best method. I have tried it in many project and it worked well. If u write code properly very little processor time will be consumed for ISR. Morover this method has adv of having counter of any lenght 8 bit , 16 bit & more. One more adv of this method is debouncing i.e. generally pulses from real time sources have glitches during trans phase (0 to 1 & 1 to 0) which cause hardware timer/counter incres multple time for one pulse. Since pulses he is getting is from real time event there is no poss of 50 usec pulse and that can be solved by monoshots.
One method to override narrow pulses proble is counting using Intrpt i.e. input countng pulses to intrpt lines and count do soft counting during intprt.

Anil