They are extra setting to fine tune your (PU) processing unit. In my example, these are my flags (settings) for one of my 6850s "-v -w128 -f0". Off the top of my head, they mean something like this:
v = VectorsThis allows vectors to be used. I think 0, 1, 2, and 4 are the settings for other miner programs. GUI miner auto uses the best vector setting. Adding this flag can increase your hash rate.
w = WorksizeThis is the size of the work flow into your PU. Certain GPUs and CPU use certain settings. 128 is the sweet spot my 6850s, but 256 is the sweet spot for my 5850s.
f = Frame RateThis will try to make sure you are constantly getting at least a certain amount of frames on your desktop. In the pic above, my second videocard doesn't run my desktop. So it's not important, and I keep that set at "0". However, for my first videocard I keep it at "100" to keep a somewhat steady 100 Frames Per Second running on my desktop. (Protip: The human eye can't notice anything above 72fps as long as it's consistent.)
Consult this guide to get a ballpark idea for the flags that work for you:
https://en.bitcoin.it/wiki/Mining_hardware_comparisontl;dr
v turns on Vector. w is the worksize. f is for your fps.
EDIT: These are the flags for the poclbm kernal (which I think is default for GUIminer). jojo posted an example of flags for the phatk and phatk2 kernal.