1) Define the Super-Hero. Superman has superspeed, immunity to almost everything (except Kryptonite and... MAGIC!), supervision, superhearing, laservision, immunity to disease & poison, adaptability to heat, cold, pressure, radiation, acid, etc., etc., ad nauseum, the ability to leap and fly, etc. What does this PC have?
Once you know, give him the abilities that he needs to do it, in game. DR Infinity/Kryptonite or Magic, immunities, Swim & Fly speeds, faster movement rates, At-Will "Spell" usage (which can be cancelled in Anti-Magic Spheres), (Ex.) Abilities, etc.
So you want to get rid of the equipment problems? Free Monk levels do a lot, as does Improved Grapple. You can also give him "Force-Armor" and an appropriate "Weapon of Force" which are weighless, work against Immaterial/Incorporeal creatures, and are always present, and/or his natural weapons function under an (Ex.) Ability similar to the
Greater Magic Fang spell. Later, allow him to imbue them with
Bane,
Holy, and/or other qualities.
The D&D version of "Spider-Man", for instance, gets Constantly-On
Bull's Strength, and At-Will use of
Spider-Climb and
Web (as well as some (Ex.) "Swinger" Abilities).
2) Carefully consider what the PC CAN'T do... Supers who AREN'T immune to poison & disease are easily taken out! Those without Fast Healing/Regeneration won't last much longer than usual! Those not immune to Negative Energy will become Undead, soon enough!
Even in a Supers campaign where I created a hero pretty much immune to EVERYTHING, that didn't solve his problems! Once, while charging an Autocannon, he found that, while the 50mm shells couldn't hurt him, he was being knocked back further than he could run, and thus never got anywhere close to his target, so he couldn't smash it! In another episode, a Super-Villian picked up a big chunk of concrete and threw it at him... While the hit did him no harm, my PC's normal STR was insufficient to LIFT it, and he was PINNED by the block (fortunately, he had a burrow speed, but by the time he managed to dig his way out, the fight was over)!
In other words, everybody has problems! Even if you can
Teleport Without Error, at will, you still can only go where you have already been, or can see. It DOES make equipment less important, though!
3) Consider the Weakness(es).
Smallville had a Freak-of-the-Weak who made a Kryptonite bullet, and shot Clark with it. I've been WAITING for this to happen! Likewise, it is OBVIOUS that Mordent, the Super-Mage, has a weakness of
Anti-Magic Shell. (Ex.) Super-STR Hercules isn't immune to Paralyzation (good thing he never fought Ghouls, huh?)
You might also want to tie in weaknesses to Super-Powers... How many times has a superhearing PC had problems with a Sonic attack? How do supersmelling PCs respond to Ghasts?!?
With all the energy types (which DR does NOT effect - See Energy Resistance), different attack types, etc., no Super-D&Der will be immune to everything! Hercules, besides Paralyzation problems, would have a heck of a time with
Telekinesis and/or
Reverse Gravity! ("AHHHHHhhhhhh!!!" <ThwumpPP!>)
Figure out some way to make your Player's PC immune to what he needs to be immune to, and then use his weakness(es) to allow the Super-Villian to make his abilities not matter... Herc, again, encountered a son of some earthy goddess who he killed, like, three times, who kept regenerating while in contact with the earth. In order to defeat him, he had to lift him off the ground, and tear him apart, there.
4) Knockbacks. In supers games, PCs get knocked back, into (and THROUGH!) things, all the time! Institue a Knockback rule... For every 5 HP of damage a character takes, he is knocked back one foot. Knockbacks of 5' or less simply become a 5' step. 6'+ requires a DC:20 Balance check (or Reflex save), or you fall down (AoO provoked by rising)! Being knocked back into objects does falling damage (1D3/5'). This does half damage to the character, and half to the object hit.
Stoneskin, DR, etc., as well as armor, absorb some of this damage, acting as Hardness.
I think that should just about do it! Now pass out some free Feats to Supers (Heroes as well as Villians), to make combat the style you want (Dodge, Mobility, Spring Attack, Fly-by Attack, Improved Unarmed Strike, Improved Grapple, Captain America's Shield Feats, etc.), and you're there! (I think there's even a knockback-style Feat for Giants!)
Have fun!
