first thing to do is chuck an injector cleaner in your fuel tank (use a diesel one )use it double strenth and put it in, run for half an hour to get it round system, leave for a day to work on stubborn deposits then run tank to near empty before refilling. don't run out!!
http://cgi.ebay.co.uk/Redex-Diesel-Fuel-System -Cleaner-injector-cleaner_W0QQitemZ22023646905 0QQihZ012QQcategoryZ28641QQssPageNameZWDVWQQrd Z1QQcmdZViewItem
after that it's injectors or pump usually.
does it run rough at tick over? if yes : crack open each pipe to the injector, one at a time, and see if it alters the tick over. if no change or very little change compared to the other three when they are done it'll be that one.
if it's the pump it needs doing by a specialist company, they aren't really a diy job to repair/refurbish.