Sonic Pistol vs. Gauss Rifle
Overview
The Sonic Pistol and Gauss Rifle are the two generally-suggested general-issue weapons, since the Gauss Rifle is obviously better than any other non-alien weaponry, and the Sonic Pistol is better for an assault role than any other alien weapon due to its lower TU cost.
Obviously, there are weapons that surpass both of these in some roles, e.g. the Sonic Cannon for a sniper rifle, the Dart Gun for training reactions and the Disruptor Pulse Launcher and Sonic Pulser for splash damage and terrain destruction. However, none of these really work as a standard weapon assuming you have a choice.
The Stats
Aimed mode: 60% TUs for 100% base accuracy
Snap mode: 30% TUs for 65% base accuracy
Auto mode: 40% TUs for 50% base accuracy
60 Gauss damage
Aimed mode: 50% TUs for 85% base accuracy
Snap mode: 30% TUs for 65% base accuracy
80 Sonic damage
Basic Analysis
In general, using these weapons in an assault role involves the Auto mode for the Gauss Rifle and the Snap mode for the Sonic Pistol. There are two general situations of use: point-blank and non-point-blank. The difference is that accuracy hardly matters at point-blank range since it's nigh-impossible to miss.
Point-blank calculations:
Gauss Rifle: 6 shots/turn @ 60 damage = 360 damage per turn
Sonic Pistol: 3 shots/turn @ 80 damage = 240 damage per turn
Non-point-blank calculations:
Gauss Rifle: 6 shots/turn @ 60 damage each and 50% accuracy = 180 on-target damage per turn before soldier accuracy
Sonic Pistol: 3 shots/turn @ 80 damage each and 65% accuracy = 156 on-target damage per turn before soldier accuracy
Intermediate Analysis
[To be added]
Advanced Analysis
[To be added]
Verdict
The Sonic Pistol is better against Lobster Men, Tasoths, and (more narrowly) Gill Men, and due to the immense disparity against the first two is the better to take on an unknown-race mission (e.g. Ship Rescue Mission, or simple lack of a Transmission Resolver). However, the Gauss Rifle is generally better against Aquatoids as long as you have some other means of disposing of any terror units.