Armour:
Most modded metals can be crafted into armour or weapons in a pinch. Bronze is cheap and frees up iron for progressing other mods.
Most midgame sets are good when you get them, but don't invest into fully upgrading something like Dark Steel if you intend to replace it anytime soon.
Fully socketed Bound Armour is great direct defense, can be augmented with some utility and TC runic shielding
Terrasteel offers some unique endgame upgrades, those are a pain to get though
Ichorcloth Robes basically are magical Quantum Armour, and unlike most other options they don't require any maintenance/power supply once you have them
Last Stand enchantment+XP farm=practical immortality, in general properly enchanted armour is way better than non-enchantable sets once you can afford them, unless you need a specific functionality of course
Weapons:
TiCon all the way, unless you really like a specific feature from another mod (extra Ender Pearl drops, Weak Blood Shards if you can't be bothered to automate slates etc.) bronze and steel are easy to get with the default configs and in some ways better than their TiCon-only equivalent (Steel in particular was better than Alumite in just about every way last time I checked)
Most fully upgraded melee weapons are very close in damage, so it's more about costs and special perks. TiCon rapiers against armour, cutlass for extra crits (good for Terrasteel "Will of..." procs), anything else for special effects. The Awakened Ichorium Sword has an AoE attack similar to TiCon scythes, the Sword of the Zephyr, Cursed Spirit's Blade and TiCon longswords give extra mobility, Botania swords have a decently harmful ranged attack option.
For ranged attacks the Mining Laser does good damage and AoE, but wrecks the terrain. Nothing really beats an ExtraTiC crossbow (Signalum limb, Enderium or modifier-loaded bolts) in terms of raw power though.
Blood Magic spells or the Energy Bazooka are fun to use, albeit not very practical for their cost most of the time
The TC Shock focus bypasses most forms of projectile defense and can be upgraded to endgame-level damage. Amber cores regenerate vis insanely quickly and Elementium caps give a massive casting discount, second only to Ichorium
Botania's Mana Blaster makes a nice "infinite ammo" ranged weapon when it first becomes available and can be augmented to bounce off walls or pierce right through them, but sadly there's no way to increase its damage. The TTKami Shadowbeam focus offers a stronger "bouncing" weapon
If you don't like Thaumcraft enchanting EnderIO's Enchanter can produce books, BiblioCraft's printing press can copy them for xp (cheaper material cost than the Enchanter for getting higher levels, but you need a good xp farm either way) and Botania's Mana Enchanter lets you pay the obscene costs of over-enchanted gear in mana instead of xp or essentia. Make sure you get the TC addon enchantments for your weapons though, you need them to keep up with TiCon+ExtraTiC crazyness. Keep an MFR Disenchanter or some Spellbinding Cloth at hand too.
Support/Baubles:
If you really want to min-max, first of all check which effects can be gained without sacrificing a Bauble slot. ExtraUtils famously gives creative flight with no strings attached, some armours innately give fire, drowning, hunger and/or fall damage mitigation.
Tainted Blood Pendants (Botania) are good for permanent potion effects, and one relic ring combines a health boost with several immunities in a single item. The knockback nullifier can also help a lot in some fights. Don't use rings to hold mana if you have a reliable automatic production system, just bind a Mana Mirror to your main pool. All Botania baubles can be augmented with TC runic shielding (except maybe the relics, haven't tried those yet)
Thaumcraft(+addons) provides a lot of utility effects, such as another knockback nullifier, hunger management, status cleansing (removes Wither unless something changed!), full Creeper immunity and more. There's no god-item to combine them all, but if you have trouble with a specific mechanic try flicking through the Thaumonomicon if Botania doesn't have a solution
Blood Magic and Botania both have very good multi-use potions for boss fights
Before you get all the uber-endgame stuff remember there are cheap options for fast movement (TC boots, Botania sash etc.), semi-flight (jetpacks, gliders) and other combat/survival-relevant effects
And last, don't forget vanilla mechanics! Milk cleanses potion effects, Golden Apples give a ton of buffs (and are much more affordable with a modded Pigman/drop melter/laser drill gold farm) and Ender Pearls can get you out of a tight spot if you don't carry an EnderIO staff or Blink focus
