I hope you notice that so far the advice from any one post on this thread is at best only slightly compatible with any other post. That's fine; people have different ideas of what is fun. But my first bit of advice is don't try to please everybody! Whether you want skills to be freeform or codified, trait-like and binary or level-able and continuous; it's all fine, except you can't have it all and will have to decide what kind of skill system you prefer.
Now for some more incongruous advice on skill systems:
-Try to use similar rules for similar skills. I find it cumbersome to, for example, have different sorts of modifiers for balancing, jumping, or riding, when similar conditions would impact all those skills. For my own amusement I recently reworked the Pathfinder skills and discovered I could group skills by type (e.g. movement skills, social skills, knowledge skills, etc.) and use general rules for each type, then describe how each individual skill uses those general rules or varies their application. I found it makes the skills chapter shorter, more cohesive, and easier to understand; and is much better than if each skill is its own subsystem.
-I echo TKDB's point that each skill should have roughly equal value. That value will be somewhat subjective, but something like the classic Profession (underwater basket weaving) will never be used as often as Acrobatics or Bluff. The corollary is to make sure skills have a good, common in-game use. Leave flavorful stuff for another mechanic, if you bother with a mechanical representation at all.
-Make it easy for the GM to adjudicate skill uses by providing generic modifiers to the difficulty of a skill check, though you can also provide some specifics. Something like: "Significant hazard (such as a slippery surface, or blustery wind): +5".
-A neat rule from Iron Heroes: If you use subskills (like the various Perform or Profession skills in d20 games), consider not tracking each skill individually. Rather, let the player buy one point for each subskill, then let each subskill advance at the same rate. For example, a player could spend one point to get Perform (percussion), another to get Perform (strings), and another skill point to advance both subskills by +1.