Ripper or flame thrower. I find ripper slightly better, more efficient and certainly more fun weapon, but they both become useless when black monsters start to dominate along with speedy ones. Plus there is the "getting the ammo you don't need" issue to fuel your ammo problems.
Now I played on normal mode, so perhaps there is some difference, but I did notice that I virtually always got ammo only for the weapons I had equipped. When I finished the game I had excessive amounts of ammo for all my primary weapons. That is: plasma cutter, ripper, contact gun, line gun. Combined with the fact that ammo resets to one on any weapons you store in the safe (but only between loads), it made it a real pain if you want to change your weapon set for a particular level or area. You really have no choice but to stick with the same 4 guns the entire game, or else spend lots of money on new ammo every time you change your set.
I probably used the ripper the most, even at the end. I found that because it holds the enemy at bay, as long as your back is to a wall, it's rare to take damage until the ripper has had enough time to kill the enemy. If there is a lot of guys, just stand in a doorway while quickly sweeping back and forth, and they can't touch you. Also, you can fire a new blade before the current one expires, so you never have an opening. For those times where I messed up or was in a bad position, I took them out with a few shots of the line gun. I used the plasma cutter mainly for distance work, and the contact gun for big enemies. Worked out very well, I only died a handful of times.
It took me just under 20h to complete, but keep in mind I took a fairly slow completionist pace. For example, I translated almost all the graffiti I found. I can just about read the stuff without a reference now. Although, I didn't get the secret code, I'll probably do that the next play through.
Oh, the free level 5 suit from PS Store really helps too. Never had inventory troubles. But now that I have the level 6 suit unlocked, I'll be using that. Reminds me of the Combine uniforms from HL2.