What are the best (non-core) base classes?
The marshal adds an interesting dynamic to the game that doesn't really exist in the core rules. It sort of mirrors by the bard, but not exactly. The Tome of Battle and Tome of Magic are great fun to introduce, but you do have to be careful with Tome of Battle. Used judiciously, it adds an extra element of fun to the game. Used abusively, it will wreck game balance.
What are the best (non-core) +0 LA races?
I'm a big fan of the Eberron races. The shifter, warforged, kalashtar, and changeling all bring something really different to the campaign, especially the warforged and changeling.
That's really hard to quantify. Feats are largely a matter of taste for most players. Every player has their pet feats which they feel are awesome and better than everything else, but almost any feat taken with a proper amount of strategy in mind works well. I will say that one class of feats has been a real game-changer, the Reserve feats. Some might say that spellcasters didn't need more power, but especially at low-levels, these give casters a defining element while at the same time giving them something more to do than fire a crossbow. And I think the Martial feats from Tome of Battle should be available to all classes, Psionic feats should be available to monks, and Sudden Metamagic feats should be banned outright (as should Divine Metamagic and virtually anything else that grants "free" metamagic).
What are the best spells?
All of them. Spells are inherently better than anything else in the game because every spell is an exception to the rules in an exception-based rules system. The more you have of them, the better you are. Thus, the cleric and wizard are the best classes in the game because they get the most. I'm not sure otherwise how to answer that question.
What are the best magic items?
I like the MIC approach to including a lot of lesser magic items that are usable for PCs at lower levels. It gives lower level PCs more to look forward to than a simple +1 weapon or +1 shield. Plus it emphasizes items with nifty effects instead of static bonuses. Nifty effects are almost always more exciting than static bonuses (even though powergamers generally prefer static bonuses).
What are the best monsters?
As recurring villains, I have always loved the mind flayers. They are inscrutable, devious, and cunning, and there are all sorts of supplemental material for them. There is the Lords of Madness supplement which gives all sorts of juicy information on them. Plus there are the Mind Flayers of Thoon from MMV.
As one of the more middling races, I am very fond of jermlaine (MM2) and their mischievous ways. They may not be very impressive one-on-one, but a horde of them can do incredible things for plots in your games. Items go missing in cities, people disappear (captured Lilliputian-style), and people are pointing their fingers at halflings, but meanwhile it's all a sinister plot of the jermlaine sorcerer who thinks he's become king of the underworld.
Rather than specific monsters, I find cults to be a great source of inspiration for recurring villains. The cult of Vecna is my favorite (and a Greyhawk staple), but a war-centric campaign could feature Hextor or Erythnul. The Age of Worms adventure path did a great job of making the return of Kyuss a scary plot arc.
What's the best setting content?
If 3.5 is your game then Eberron is your setting. It's the only setting designed with 3.5 in mind. Every other setting before had to be molded and reshaped to fit the preconceptions of 3.5 (like NPC classes to name one), but with Eberron, they had a clean slate, and everything blends seamlessly. I generally don't run 3.5 anymore unless its in the Eberron setting.
What are the best adventures?
For 3.5 look no further than Paizo's three adventure paths, The Shackled City, Age of Worms, and Savage Tide. My personal favorite is the Age of Worms, which sees the PCs battle an evil cult which is determined to release its imprisoned god and bring him to power over all the world. Shackled City is a close second. It has a very personal feel to it and the campaign is open-ended offering the PCs a great chance to make their stamp on the world as they battle a group of maniacal villains intent on manifesting the prison plane of Carceri on the Material Plane and using it to further their vile ends. The Savage Tide is a great campaign too. It is my least favorite though because it is a swashbuckling type adventure with lots of high-seas action and I could just never get into that outside of watching Pirates of the Caribbean. WotC produced an "adventure path" of sorts for 3.0 following the release of the game which is a pretty good series of adventures, but they lack anything more than a few ephemeral tie-ins to each other.
What are the best variant rules?
One that I always use now is the Upkeep variant from the DMG. It just puts little things like paying for your stay at the inn or buying a round of drinks on the down-low and lets you get to action like smashing in dungeon doors. I also like the Weapon Groups variant from Unearthed Arcana because it is a throw-back to AD&D, but I like a lot of things about AD&D so that's why. I also strongly recommend using
Pathfinder's Combat Maneuver Bonus in place of things like Grapple or Disarm checks. Its a streamlined system for these things that just makes everything a lot easier.
