Look here for answers to any rules or crunch questions that come up often enough to require public clarification.

Skill Checks and Saving Throws:
In general, I will roll most of your saving throws for you in order to preserve and support the flow of play. You may be informed of the save results, allowing you to react appropriately in character, or you may (in the case of something like a fireball) simply be told what happens (as possible responses are limited). This will vary from situation to situation, but a good rule of thumb is, if you are not asked to roll a saving throw, then I will be doing it for you. If I want you to do it, yourself, I will request it directly.

Likewise for certain skill checks. Players will never roll Appraise, Disable Device, or Sense Motive checks; these three skills will always be rolled by me, unless there are extraordinary extenuating circumstances (such as certain special abilities acquired through feats or class features). Other skills will generally be rolled by you; the determining factor is largely a question of active versus reactive.

For example, if a Knowledge skill you possess is relevant to a creature, clue, or other stimulus encountered in the course of play, I will roll it for you and inform you of what your character knows. If you do not receive Knowledge check results, then your PC does not know anything, and you should not roll Knowledge to see if they do (because I have already done it in the background). However, if your character is performing research in a library, then you would be the one to roll a Knowledge check, and I would simply tell you what happens, as a result. This division of responsibility can be applied to the commonsense functions of most multifunctional skills: I will roll Linguistics for you if you encounter a forged document, but you will roll Linguistics for yourself if you are trying to create one. I will roll Disguise for you if someone tries to see through your charade, but you will roll Disguise for yourself if you are attempting to conceal an ally's identity, and so on.

Again, the short version is: If you need to roll, you will usually be asked to, but you can assume it is your job to roll when you are actively using any saving throw or skill (other than Appraise, Disable Device, and Sense Motive) with an active function. If the saving throw or skill check is reactive, then I will probably roll it for you and inform you of the results (or I will tell you we are doing something different).