Realistic Equivalents (TFTD)
- Dart Gun
- Heckler & Koch P11 Underwater Pistol  This is the actual Dart Gun! 5 shot / 5 barrel. 10m-15m range underwater, 30m on land. Fires 10cm darts. Not reloadable in the field.
- Other Pistol-type weapons
- Jet Harpoon
- РПБ-1М pneumatic 'military spec' speargun. 5m range, single shot, not terribly effective! 
- Other Rifle-type weapons
- APS Assault Rifle . Older underwater assault rifle. More effective than spearguns. Effective underwater range 11m-30m (dependent on depth). Difficult to use, power similar to a normal pistol, less effective than normal firearms above water - 50m range, limited lifespan. 26 round magazine. (Not clear if auto fire works underwater).
- ADS Assault Rifle . . New selective fire underwater assault rifle based on the A-91M. 18m-25m effective range underwater (dependent on depth). Uses a very elongated, pointed bullet. Genuinely dual-use (water/land). Can fire normal ammunition very effectively above the water, uses standard magazines, and standard ammunition above-water. 30 round magazine. Grenade launcher and accessory capability. (Not clear if auto fire and the grenade launcher work underwater).
- PNW MEA underwater rifle ammunition in 7.62x51mm NATO. Standard NATO bullet travels 2 feet underwater, this has an effective range of 30m. There is also a variant of the ammunition with very high antipersonnel damage. 
- Mk 40 Mod 0/1. Anti personnel depth charge. 
- MAXAM EXPAL GAB Underwater Grenade. For anti-diver use. 
- [E-105 fragmentation grenade. http://www.pmulcahy.com/hand_grenades/british_hg.htm]
- M67 grenade (possibly just for surface use by frogmen?) 
- M14 incendiary thermite grenade. A demolition type of grenade for underwater use. 
- Dye/Smoke Grenades
- Seems to be a consensus that smoke grenades would not work
- Can't find anything like a dye grenade...
- Underwater Demolition Charges
- Many types and models exist...
- Gas Cannon / Hydro Jet Cannon
- Arsenal RLV-AD anti-diver 40mm grenade round. Not clear if it can be fired under water, or needs to be fired into water. 
- MRG-1 MULTIBARREL ROCKET GRENADE LAUNCHER with RG-55M-1 rocket grenade and the UG-45 universal grenade to engage frogmen. (Link broken)
- Torpedo Launcher
- Can't find any frogman-launched torpedoes...
- Gauss Weapons
- Coilgun pistols are available now that fire .25 projectiles (similar to the HK P11 dart gun) at a claimed 180 fps in air.  
- Hobby rifle-type coilguns get up to 25J kinetic energy, which exceeds most countries' legal limits for air rifles (where such limits exist). This link for a coilgun rifle is one of the best. 25J with plans on the table for a nearly 100J version, which is the muzzle energy of a ridiculously powerful air rifle or a weak firearm. Coilguns actually favour high mass, long, low velocity projectiles (think spears), which could be much more appropriate for underwater use. 
- Of course muzzle velocity/energy is going to be considerably reduced in water, even with a very hydrodynamic projectile. Obviously more electrical energy is needed! But submarine research in particular, is always trying to up the energy density of portable power sources. By the time we get to 2040, who knows!
- Craft Gas Cannon
- Light Gas Gun. Up to 7km/s in air. Might attain respectable speed underwater with a properly hydrodynamic ("hypersonic" in water) AP projectile. 8km range might be achievable after all. http://en.wikipedia.org/wiki/Light_gas_gun
- D.U.P. Head Torpedo - Depleted Uranium has been successfully used in Military Applications as a material for Tank Armor and Armor-Piercing Munitions. However, the use of Depleted Uranium has not gone without controversy as it is a toxic metal that has detrimental long-term effects on both human health and the earth's environment.
- Craft Gauss Weapons
- An underwater Railgun  or Coilgun ("Gauss Gun")  ? Navies are working on these for surface use. Might solve some of the cooling problems. A (presumably) nuclear powered sub would have plenty of power on hand to run either type of electromagnetic weapon. The projectile issues are no different than the Gas Cannon, once you've got the required muzzle exit velocity.
- Craft Sonic Weapons
- US Navy patent for remote cavitation-inducing undersea energy weapon