The cat threads across the various forums are littered with people asking questions about what gems and enchants should be used, and how to reforge. The advice is varied and in many cases out of date as people have not fully embraced the changes that 4.06 made. The following three rules are all you need. If you spend more time thinking about gemming, enchanting and reforging than the amount of time it takes to read this post, you are spending your time on the wrong subject. You would be better suiting thinking about your rotation and the various boss encounters your guild is working on if you want to make significant improvements to your dps.
1. Always gem for agility. Agility is generally worth about three times the stat value of any of the secondary stats. Unless a socket bonus is worth 14+ agility for a single gem socket, ignore it. In the current content there are only a few items in the game where it is worthwhile to get the socket bonus (helms, tier chest, Sinestra belt). Everything else should be gemmed with agility (delicate). As it happens, in all three cases where it is worth getting the socket bonus, the socket color is blue – so you will be using agility/hit gems for the blue sockets in those items (glinting).
2. Use the known BiS enchants. The BiS enchants are well understood. Agility/haste for the helm; agility/mastery for the shoulders; agility for the back*, bracers, weapon and boots; stats for the chest; Attack power/crit for the legs; strength for the gloves. Don’t use any other enchants. * 65 crit is a viable alternative for the back.
3. Get mastery on every item. Mastery continues to be the best of the secondary stats and is generally worth about 20% more than the other secondary stats. If an item does not have mastery on it, reforge the highest available secondary stat to mastery. Per my post 4.06 – the Homogenization of Secondary Stats the difference in relative values of all of the secondary stats other than mastery are pretty close and varying them will have minimal impact on your dps. Once you have mastery on every item, then you can reforge selectively as needed (hit until 4.1 for interrupts) or desired (for example some people like to reforge to expertise on Al’akir). In general having haste and crit balanced provides good results, although some people prefer to reforge to hit/expertise in order to have a more stable rotation and consistent results on fights with target switching.