I made a chart, for myself, on natural dps for each weapon. It seems that the highest dps weapons are newer and more difficult to make. On average a Radient Scimitar will out DPS the Cutlass/Katana/Wakizashi(all the same DPS) by about 2-3 DPS(with dmg bonus from 100 Str, Dex, Tact, Anat, Item Property DI). However the Cutlass & Katana, at least, are guarenteed to be GM quality. Radients are a roll of the dice for GM quality.
The Crescent Blade generally has the highest DPS for 2-Handed Swords, with the Rune Blade and Daisho hardly ever more than 2 DPS behind, they even occasionally have higher DPS. The Bladed Staff is, on avg, 2-4.5 DPS behind the highest at each level.
The Mace is very rarely more than 1 DPS behind the Diamond Mace, yet GM quality is guaranteed. The Mace occasionally has a higher DPS with the right Dex/SSI combo.
The Tessen swings at max swing speed with only 90 Dex, or 60 Dex and 5%SSI, and easily out dmgs every other weapon at that level. Since it's at max, there is no way to up the DPS by Dex/SSI. Quarter Staves, made of Ash, swing at max speed and have a pretty nice DPS, yet still not as high as the Tessen.
Short Spear out dmgs Assassin Spike and Kryss by about 1.5. All 3 swing at max swing speed at 90 Dex, so no SSI will ever improve the DPS(SSI will help stay at max sing speed when Stam is below 90). The War Fork can out dmg all 3 of them with 90 Dex & 20 SSI(or 120 Dex & 5% SSI). The Double Bladed Staff can match the War Forks DPS with only 90 Dex and 5% SSI (or 120 Dex). The Leaf Blade, Spear & Pike can really dish out DPS at higher levels of Dex and SSI.
For Archery weapons... the highest DPS 4 are Crossbow, Repeating Crossbow, Heavy Crossbow, Magical Shortbow, Bow(more or less that order). The Bow is rarely more than 2 DPS behind the highest DPS.
Oddly enough the highest DPS Axe is the Hatchet(non-Runic-able). The Ornate Axe has the highest DPS at low and extremely high Stam/SSI levels. Surprisingly the 'Axe' out dmgs the Ornate in between.
This list is based on each weapons DPS derived from the weapons Base properties(min/max dmg and speed) and any stat and skill dmg bonuses. Each weapons final item properties(HCI, Hit Spell) & each targets resists will vary actual damage output. I hope this research helps more than it confuses!