The problem isn't so much that Magic Missile is too good, it's that other 1st-level attack spells in 3rd Edition suck most of the time. Burning Hands and Chill Touch can be useful once in a while, but do too little damage at too great a risk to the caster, until around 4th/5th level. Use Burning Hands to maim 4 goblins? As a 1st-level caster, you might not make the Concentration check to avoid an AoO. Even if you do, the goblins will kill you next round with their morningstars. You could do better than BH with a dart, and from a distance.
A 1st-level wizard has maybe 2-3 1st-level slots; if you spend 1 for Mage Armor, chances are your AC is still only about 14-16. 4 goblins attacking you will likely get at least 1 or 2 hits, and one or two 1d8-damage hits will knock the wizard unconscious; if that's the first attack, the others will likely all hit because the wizard will have fallen prone, and thus finish off Mr. Wizard. Burning Hands needs to deal better damage at 1st-level at least, and same with Shocking Grasp (Chill Touch perhaps, but it does have its handy 2nd function). The only reason Magic Missile is used so much (all 3 sorcerers in my Rhunaria homebrew campaign have it, though only 1 uses it often), is that other low-level spells aren't so good for controlled attacks. Fireball could hurt allies or cause other collateral damage. Flaming Sphere is half-likely to do squat (in all the years I've been using that spell or seen it used, it's hardly ever actually done damage). Acid Arrow is nice (and Scorching Ray is too nice in 3.5), but attack rolls and gradual damage aren't very good for mages sometimes. Other low-level blaster spells need melee range. In my games, at least the players (myself included when I'm not DMing) describe their Magic Missiles flavorfully.
Anyway, for some variety, you could perhaps try some of these homebrew spells of mine. These are from a variety of settings and characters; I've never had more than a few of these in any one game.
Chromatic Ray
Conjuration (Creation) (Acid, Cold, Electricity, Fire, or Sonic)
Level: Sor/Wiz 1
Components: V, S
Casting Time: 1 full round
Range: Close (25 ft. + 5 ft./2 levels)
Effect: Ray
Duration: Instantaneous
Saving Throw: None, or Fortitude partial, or Fortitude negates (see text)
Spell Resistance: Yes
The Chromatic Ray spell projects a beam of light at one target creature within range, and the light rapidly fluctuates as it switches from one color of the rainbow to another. As a ray spell, you must succeed at a ranged touch attack to affect the target. If you hit, you must roll 1d6 to determine what color the ray was when it struck, as this determines what effect the ray has. The ray is blue on a 1, green on a 2, yellow on a 3, orange on a 4, red on a 5, or violet on a 6. If the ray is blue when it strikes, the target suffers 1d4 cold damage and must attempt a Fortitude save, which causes them 1 point of temporary Strength damage if they fail the save. If the ray is green when it strikes, the target must attempt a Fortitude save, or else be poisoned and suffer 1d2 points of temporary Dexterity damage as the poison's initial effect, and if the first save is failed, they must attempt another Fortitude save 1 minute later or suffer 1d2 points of temporary Dexterity damage as the poison's secondary effect.
If the ray is yellow when it strikes, the target suffers 1d3 electricity damage and must attempt a Fortitude save, which stuns them for 2 rounds if they fail the save. A stunned creature cannot act and loses any Dexterity bonus to AC, while attackers get a +2 bonus on attack rolls against a stunned creature. If the ray is orange when it strikes, the target suffers 1d6 acid damage. If the ray is red when it strikes, the target suffers 1d2 fire damage, while any nonmagical flammables and combustibles upon the target's person will ignite, and the character suffers 1 more fire damage each round that such materials burn on them, until they extinguish the flames or remove the burning items. If the ray is violet when it strikes, the target suffers 1d4 sonic damage and must attempt a Fortitude save or else be deafened for 5 rounds. This spell has either the Acid, Cold, Electricity, Fire, or Sonic descriptor, depending on which color the ray is when it hits.
(This is an old spell I made early on in 3E, and could probably use a bit of damage or level scaling added in)
Force Spike
Evocation (Force)
Level: Sor/Wiz 1, Wuj 1
Components: V, S
Casting Time: 1 action
Range: Close (25 ft. + 5 ft./2 levels)
Effect: Ray
Duration: Instantaneous
Saving Throw: None
Spell Resistance: Yes
You point a finger at one target within range and unleash a powerful, dart-sized needle of force at them. As a ray spell, you must succeed at a ranged touch attack in order to affect the target. On a hit, the target suffers 1d8 piercing damage, +1d4 piercing damage per five caster levels, to a maximum of 1d8+4d4 piercing damage at 20th-level. As a special quality of Force Spike, this ray has a threat range of 18-20, and a critical multiplier of x3. Thus, it scores a critical threat on a natural attack roll of 18, 19, or 20, and if a threat confirmation roll for such a critical threat is successful, roll the damage for the ray three times.
Glimmer Beam
Evocation (Fire) (Light)
Level: Clr 1, Dru 1, Shu 1 (Fire), Sor/Wiz 1
Components: V, F
Casting Time: 1 action
Range: Medium (100 ft. + 10 ft./level)
Effect: Ray
Duration: Instantaneous
Saving Throw: Reflex partial
Spell Resistance: Yes
The Glimmer Beam spell unleahes a bright, shimmering, blinding ray of light from one of your eyes, striking at a single target creature or object within range. As a ray spell, you must succeed at a ranged touch attack to affect the target. On a hit, the target suffers 1d6 fire damage, +1 fire damage per three caster levels, to a maximum of 1d6+6 damage at 18th-level. The base fire damage is instead 1d10 if the target is undead, since a small amount of positive energy is channeled in the beam of light, so the maximum damage against an undead creature is 1d10+6 by 18th-level. A creature stricken by the Glimmer Beam must succeed at a Reflex save or be blinded for 5 rounds, then dazzled for another 5 rounds after that. Aside from the obvious effects, a blinded creature suffers a 50% miss chance in combat (all opponents have full concealment), loses any Dexterity bonus to AC, grants a +2 bonus to the attack rolls of others who are attacking them (the attackers are effectively invisible to the blinded creature), moves at half speed, and suffers a -4 penalty on most Strength- and Dexterity-based skills. A dazzled creature merely suffers a -1 penalty on attack rolls.
Static Orb
Evocation (Electricity)
Level: Dru 1, Sor/Wiz 1, Wuj 1
Components: V, S
Casting Time: 1 full round
Range: Medium (100 ft. + 10 ft./level)
Target: One creature
Duration: Instantaneous
Saving Throw: Fortitude partial
Spell Resistance: Yes
This spell launches a globe of static electricity at one creature you designate, homing in on them and applying a shock across their body. Static Orb deals 1d4 electricity damage to the target, +1d4 electricity damage per six caster levels, to a maximum of 4d4 electricity damage by 18th-level. The target is also dazzled for 1 round per Static Orb damage die, but does receive a Fortitude save for half damage. A dazzled creature suffers -1 on attack rolls as their eyes are overstimulated by the bright electricity flashing before them. In addition, on a failed save, the target is stunned for 1 round, plus 1 round per Static Orb damage die. A stunned creature cannot act and loses any Dexterity bonus to AC, while attackers receive a +2 bonus on attack rolls against a stunned creature.
Acidic Projectile
Conjuration (Creation) [Acid]
Level: Sor/Wiz 1
Components: V, S
Casting Time: 1 full round
Range: Close (25 feet, +5 feet/2 levels)
Effect: Ray
Duration: 1 round + 1 round/level, to a maximum of 5 rounds total
Saving Throw: None or Reflex partial (see text)
Spell Resistance: Yes
The Acidic Projectile cantrip transports a small, sticky orb of acidic gel to you, hovering by your hand, and you throw the gob of acid at any target within range as part of the same action. Since the acid gob hovers by your hand rather than touching it, you suffer no harm from it. However, if the Acidic Projectile hits anything within range, it splatters upon them and sticks there, rapidly dissolving some of the subject's flesh, clothing, or material. As a ray spell, the caster must succeed at a ranged attack roll to affect the target, and as a ranged touch attack it ignores armor, shield, and natural armor bonuses to AC. If the target is wearing material armor with a normal armor bonus of +5 or greater (before factoring in enhancement bonuses), a successful hit will strike the armor instead of the target, unless the caster rolls a natural 15 or higher on their attack roll.
Regardless, a successful hit with the Acidic Projectile spell inflicts 1d4 acid damage upon whatever was stricken, and then the subject suffers an additional 1d4 acid damage each round after that until the acidic gob is scraped away or loses its viscosity. If you hit anything in range, the acid gel lasts for 1 round per caster level you have, beyond the round in which this spell was cast, and the gel loses its viscosity after a maximum of 5 rounds total, becoming inert liquid. A creature may try to scrape away the acidic gel as it sticks to the subject, but this can be dangerous. Anything physical that comes into contact with the acid gel suffers 1d4 acid damage from the contact, though hardness, damage reduction, and/or acid resistance apply if the creature or object has them (as a spell effect, however, most types of damage reduction won't function against this).
If a creature tries to scrape away the acid gel with their hands, arms, or other appendages, the acid gel damages them unless they wear clothing or armor over that appendage that is sufficiently resilient as to resist all damage the acid deals, so leather gloves or the like won't help (the acid will easily dissolve the leather that comes into contact with it and thus be in contact with the creature's flesh). Scraping away the sticky acid takes a full-round action that provokes attacks of opportunity. The gel might be scraped off by using the corner of a wall or something similar, if a creature does not want to risk suffering harm themselves or to their gear while scraping off the acidic gel. In any case, if a creature scrapes away the acid gel, they must succeed at a Reflex save against this spell or the acid will remain sticking to whatever was used to scrape it from the previous subject. A successful Reflex save means the acid gob was scraped away and fell off without sticking, though it may land on the ground or the like and dissolve some of that.
Hrum. Going through some of my documents, there are some 1st-level spells I hadn't gotten around to finishing yet. But they might yield some ideas, or be finished by others....
Conjuration
(Cold) Chill Vapor: Thin fog covers 20-foot radius, incurs 10% concealment, -4 Spot, 1 point of subdual per round.
(Water) Drown: Deposits water in the lungs of a foe, may fall prone and cough fluid for 1d4+2 rounds.
(Fire) Raise Flames: Conjures mundane flames from elsewhere, 5-foot radius per caster level, for 1 round.
(Earth) Sandblast: Your hand sprays a cone of sand for 3 rounds, blinds briefly, deals up to 3d4 subdual/round.
Evocation
(Cold) Icicle Dart: Large icicle launches for ranged attack, 1d6 piercing damage, +3 cold per caster level, max +18.
(Force) Lesser Arcane Bolt: Ray of magical force deals 1d20 damage, +1 per 2 caster levels, max +5, minor backlash.
(Electricity) Shockwave: Horizontal wave 15 feet in radius deals 1d4 damage, +1 per caster level, max +6.
(Air) Whallop: Knot of wind slams into a target, 2d4 bludgeoning damage, +1 damage per level, +20 max.
Necromancy
Animate Claw: Bestow animation upon a corpse's hand, imbuing unnatural strength, control for 1 minute/level.
Bone Storm: You launch a conical hail of bone shards, 1d4+1 damage, +1d4 per three caster levels, max 3d4+1.
Lesser Enervating Ray: Ranged touch attack inflicts 1d4/level subdual damage, max 5d4, 1d4 temporary Dex damage.
Lesser Enervating Grasp: 1st-level, touch, inflicts 1d4 damage, +1 damage per two caster levels (max +2), and save versus 1d3 temporary strength damage.
Lifedraw: Draw life from a creature to yourself, deal 1d4 damage +1 per level, max +10, you heal half that.
Transmutation
(Sonic) Destructive Vibration: Target creature or object suffers 1d6 sonic damage from a sudden, severe vibration.
(Electricity) Static Flash: Sparks flare at your fingertips, foe suffers 1 damage, blindness 1 round, dazzled 1 minute.
(Wood) Thornsprout: Small plant or plant-made object sprouts large thorns for 1 minute/level.
(Acid) Vitriolic Transformation: Changes small quantity of liquid into temporary equivalent of one flask worth of acid.
