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So, just completed the game for the first time. I must say that there truly are some weapons in that thing that are just plain pointless.

Riot gun - not even that useful at mine-sweeping. Picked up for mine sweeping, then went... nah...

Rail gun - Very situational weapon. Blast radius can cause you to damage things you might not want to. Takes a lot of shots to get to the center of a Tootsie Po.... er... Cyborg Enforcer. Without getting into spoiler territory, by the time you get this (and, more importantly the ammo), the stuff you are facing kind of shrugs off the rounds.

Stun gun - umm... We aren't herding cattle here...

Perhaps this is heretical, but I'm really not a big fan of the Skorpion. Burst fire is your friend, but, for all it's vaunted glory, I find it lacking. Way, Way too much recoil for what looks to be a 9mm sub-machine gun stats wise. When your base damage/shot is in the range of the compact mini-pistol w/ teflon ugh, just ugh. From the size of the banana mags, you'd expect a bit more than that. That weapon makes me think they mashed up the CZ-Skorpion with an AK-47 to create an eldritch abomination.

Also, the "assault" rifle is rather disappointing. Where's the fire select switch? Also, 8-10 rounds in a banana mag at least 3-4 x the size of the mini-pistol mags. I wonder if that wasn't a product of CA"s firearms laws at the time. The "magnesium" rounds aren't terribly good. Magnum slugs give comparable or better performance across the spectrum of things. Only the "penetration" rounds seem to make the weapon worth it. While I'm not sure if they were around, there are some real life magnum handgun rounds that, at the ranges involved in System Shock deliver more kinetic energy on impact than a 7.62x39.

Energy weapons, outside of the Sparqbeam, aren't so hot either. Given the volumes at which the game throws ammunition at you, next time I do the game, I might not carry any energy after the first few levels. The Sparqbeam is a God-send early on, but after that energy weapons just fall flat. Given the paucity of energy charge stations, I really wonder how does SHODAN keep her seemingly endless horde of bots and 'borgs powered? Granted, I didn't play with the plasma, but the ion rifle left a lot to be desired. 'Borg target... Magnum slugs or magnesium rounds (pen rounds for the elites). Bot target... Magnum slugs or Magpulse depending on where the bot is. Oh look... that bot just dropped 24 magnum slugs... and, I still haven't found the power station... By the time I got to the bridge level, I was shooting cameras out with the Magnum and assault rifle (Mg rounds). At end-game, my character was carrying around several hundred pounds of ammunition; who needs energy weapons?
I agree there are some useless guns. I'm sure the developers had reasons for including them, but I tend to agree with you, though I did enjoy using the Skorpion on some things; it was particularly effective in the groves. I prefer the assault rifle to many other projectile guns, though I agree that it should have selective fire and more ammo capacity.
Thankfully, someone went out of their way to make a handy dandy chart of weapons for the game.