While I strongly favor having quirky spells in the game, there's no reason the direct damage spells couldn't be standardized a bit. After I posted asking WotC to come up with a model for this kind of spell, I sat down and worked one up myself.
The "power" of a direct damage spell is the sum of six variables:
1. MD10 = (Maximum Damage)/10 (X*Y of XdY, assuming the highest possible caster level)
2. EN = Energy type (elemental = 0, sonic or mixed = 0.5, force or unusual = 1)
3. SH = Shape (ray = 0, multiple targets = 0.5, line = 1, cone = 2, burst = 3)
4. RG = Range (touch = 0, close = 0.5, medium = 1, long = 1.5)
5. NOSAVE: (attack roll required = 1, no attack roll required = 2)
6. MISC: add +/- 0.5 for minor advantages/disadvantages.
Note that maximum damage typically ranges from about 30 to 120, so dividing by 10 gives a scale of 3 to 12 which is comparable to spell level.
One could certainly argue about the relative weight given to the other variables; I just fiddled with it until the values for spell power seemed to fall into line. According to the SRD, the most common direct damage spells break down like as follows (any variables with a value of zero are omitted):
level 0: Ray of Frost [MD10=0.3, RG=0.5, NOSAVE=1] power = 1.8
level 1: Burning Hands [MD10=2, SH=2] power = 4
level 1: Shocking Grasp [MD10=3, NOSAVE=1] power = 4
level 1: Magic Missile [MD10=2.5, EN=1, RG=1, SH=0.5, NOSAVE=2] power = 7
level 2: Scorching Ray [MD10=7.2, RG=0.5, SH=0.5, NOSAVE=1] power = 9.2
level 2: Acid Arrow [MD10=4.8, RG=1, NOSAVE=1, MISC=-0.5] power = 6.3
level 3: Fireball [MD10=6, RG=1.5, SH=3] power = 10.5
level 3: Lightning Bolt [MD10=6, SH=1] power = 7
level 4: Ice Storm [MD10=3, RG=1.5, SH=3, NOSAVE=2, MISC=0.5] power = 10
level 5: Cone of Cold [MD10=9, SH=2] power = 11
level 6: Chain Lightning [MD10=9, RG=1.5, SH=2.5] power = 13
level 6: Freezing Sphere [MD10=9, RG=1.5, SH=3, MISC=0.5] power = 14
level 7: DB Fireball [MD10=12, RG=1.5, SH=3, MISC=0.5] power = 17
level 8: Polar Ray [MD10=15, RG=0.5, NOSAVE=1] power = 16.5
level 8: Horrid Wilting [MD10=12, EN=1, RG=1.5] power = 14.5
level 9: Meteor Swarm [MD10=15, RG=1.5, SH=4] power = 20.5
This gives a range from about 2 to about 20, so we might decide that the appropriate power of a spell is equal to (level+1)x2. We actually find that most of the spells are pretty close to this number. Going down the list again, the spells that are generally thought to be weak or strong for their level really stand out.
Ray of Frost: target 2, actual 1.8. A bit weak. Suggestion: up damage to 1d6.
Burning Hands: target 4, actual 4. Perfect!
Shocking Grasp: target 4, actual 4. Perfect!
Magic Missile: target 4, actual 7. Too strong--make it a second-level spell.
Scorching Ray: target 6, actual 9. Also too strong, but it takes more time to get that way. Suggestion: make it a single ray that does only up to 8d6 damage.
Acid Arrow: target 6, actual 6.3. The misc. disadvantage is that damage occurs over time.
Fireball: target 8, actual 10.5. The no-brainer choice for third level, and we see why. Suggestion: at the very least, make the caster worry about AD&D-style backlash.
Lightning Bolt: target 8, actual 7. A bit weak. Maybe make it last one full round?
Ice Storm: target 10, actual 10. Perfect example of a spell with weak damage but excellent tactical advantages.
Cone of Cold: target 12, actual 11. Not bad.
Chain Lightning: target 14, actual 13. Not bad--essentially a 'lightning ball'
Freezing Sphere: target 14, actual 14. Perfect!
DB Fireball: target 16, actual 17. Not bad, it's the delay that kicks it up. Add backlash!
Polar Ray: target 18, actual 16.5. A bit weak mainly due to its short range.
Horrid Wilting: target 18, actual 14.5. Appears a bit weak, but maybe the untyped damage should be given more weight.
Meteor Swarm: target 20, actual 20.5. Perfect!
One last point: the power of a spell cannot be entirely due to damage at any level. The 3e DMG already has some guidlines on limiting damage, but not on how damage should be balanced against the other advantages of a spell.
Enjoy!