Bottomless Trap Hole and Divine Wrath also stop the Special Summoning of it from the hand via Hand of Nephthys and via Sacred Phoneix of the Nephthys's own effect as well. Stops it dead. Here is a list of cards that I've found to be viable in stopping Phoenix.
Bottomless Trap Hole
Divine Wrath
Compulsory Evacuation Device
Those cards are extremely awesome against Sacred Phoenix. First off, Evac forces them to waste two more monsters, whether that be Hand of Nephthys with another monster, two actual monsters other than HoN, using Premature Burial or other revival-type cards can really waste it. Either way, Evac blows any viable tactic out the window as they sit their and cuss to themself in their mind. Even if they pack removal cards they still will chain the card to the effect from monsters and blow that Sacred Phoenix away. Card Destruction works nicely. Since Sacred Phoenix is limited, you don't really have to worry about it that much. If you really think about it, it's basically a freaking 2400 attacking Heavy Storm. That's about all it is. It's effect hurts you just as much as your opponent most of the time unless you have a lot of cards on the field. If you know your going against a Sacred Phoenix deck, don't Set so many Spell and Trap cards and the effect will seem less threatening.