One of my favourite commands in Matrix is to specify the operating carrier of a particular sector, but this also brings up codeshares for that flight which could be cheaper.

For example: LHR O:AA JFK will bring up all AA operated flights between LHR and JFK, but if there is an IB,AY,BA code that is cheaper than the AA prime code, then this will be shown. Sometimes quite a good way to shave off some money from the fare. Also good when you know on a particular sector you want to avoid a particular operator, e.g. BA due to poor overall product on J longhaul.

MAXCONNECT 240 is another good one to limit the number of results by reducing the connection time you want - in this case to 240 minutes/4 hours. This can help Matrix find more reliable options by reducing the parameters it searches within, exactly as teledude states above - reducing the tendency to time out.