The latest 3.5 FAQ update dealt with this same question as follows:
Q: Exactly when can a character make a Reflex saving throw? The saving throw section on the Player’s Handbook says Reflex saves depend on a character’s ability to dodge out of the way. Does that mean you can’t make Reflex saves if you can’t move?
A: A character can attempt a Reflex save anytime she is subjected to an effect that allows a Reflex save. A Reflex save usually involves some dodging, but a Reflex save is not completely dependent on a character’s ability to move around. It also can depend on luck, variations in the effect that makes the save necessary in the first place, and a host of other miraculous factors that keep heroic characters in the D&D game from meeting an untimely fate.
In most cases, you make Reflex saves normally, no matter how bad your circumstances are, but there are a few conditions that interfere with Reflex saves:
• If you’ve suffered Dexterity damage or Dexterity drain, you must use your current, lower Dexterity modifier for your Reflex saves.
• If you’re cowering, you lose your Dexterity bonus (if any). The maximum Dexterity bonus you can have while cowering is +0, and that affects your Reflex
saves accordingly.
• If you’re dead, you become an object. Unattended objects can’t make saving throws.
• If you’re entangled, your effective Dexterity score drops by –4, and you must use your lower Dexterity modifier for Reflex saves.
• If you’re exhausted, your effective Strength and Dexterity scores drop by –6, and you must use your lower Dexterity modifier for Reflex saves.
• If you’re fatigued, your effective Strength and Dexterity scores drop by –2, and you must use your lower Dexterity modifier for Reflex saves.
• If you’re frightened or panicked, you have a –2 penalty on all saving throws, including Reflex saving throws.
• If you’re helpless, your Dexterity score is effectively 0. You still can make Reflex saves, but your Dexterity modifier is –5. You’re helpless whenever you are paralyzed, unconscious, or asleep.