If it is at all possible for you to let a work unit(W/U) run, then let it run. The longer it runs, the more points you will recieve when it is finished. The point system is based on clock time, not CPU time. You probably already knew this, but I wanted to encourage you to let them run. Unless you catch one early enough, you will just keep throwing time out.
One thing I do is, I have figured out that SuperOxide Dimutase(SOD) gives long W/Us. I throw them out if I see it in its first 5 hours. VGEF goes both ways(long{but never as long as SOD} and short.) I throw this one out if I see it in its first 3 hrs. I like the RAS ones. They are never long. Done in less than 4hrs usually. I haven't had a TK yet, but I hear the are out there now.
Happy Conformer Crunching!