I haven't played it for years, but some that I remember are an orange alien laser, a black hole gun near the end, the flamethrower you mentioned, a shock rifle derivative and something that I think made friendly spiders. Most of the weapons also had rather cool and unique visual effects, even the basic ones like the assault rifle. The fact that all the guns had two (often very different) firing modes, a hallmark of the Unreal games, was also good to see. This is in stark contrast to many other FPS games from the last few years, which just have several generic guns that all look and work more or less the same way (often based on real weapons and all firing hitscan, hollowpoint bullets) along with a shotgun and rocket launcher of some sort.
I found it fun to just go through the game and disregard the story because the weapons made combat in general fun and there was a ton of variation in the environments throughout the game, more than any other FPS I have played. This game scores very high on level design in my book due to this variety.