For me, one of the strengths of the Linux SMG is it's gun-butt stun. It's a stronger hit than most guns, and so that makes the Linux a better general-purpose killings/stunning weapon.
I got a fair bit of use out of the Linux SMG and the custom shooty gun. But the home-designed weapons I've stuck with for the longest would be the Death Blossom SMG and the commando rifle.
The Death Blossom SMG is a multi-function offhand weapon for my strongest melee soldiers. A chem burst of the DB-SMG can strip away a lot of armour from armoured foes (either to kill them, or to make them more valuable to stun); and the non-chem ammo is pretty good for ranged attacks.
The commando rifle is just very accurate for long-range snap shots. Its power isn't great, but it's strong enough for most enemies given that you're going to hit them essentially every time. The accuracy is so high that you can rely on it. Also, the ammo is relatively cheap to manufacture. So for a long time, I used commando rifles on most of my team for any mission where I didn't expect heavy resistance. (For things like pograms and large military ships, I'd bring some more powerful missions; but for the bulks of my missions I was using the super-cheap and super accurate commando rifles). I don't use smartrifles much, because their ammo costs more and they are less reliable than commando rifles.
In my current game, I'm phasing commando rifles out for ES lasrifles and XG rifles.
