Here's a list of lower profile and cult movies that are definitely worth your time.
The City of Lost Children
One of the more imaginative movies I've ever seen and features some of the most amazing live action sets. I definitely get the feeling the people at Irrational Games took some inspiration for the city of Rapture from this movie because there are some parallels.
Near Dark
Late 1980's Kathryn Bigelow (The Hurt Locker, Zero Dark Thirty) movie that manages to be an outlaw biker western... and vampires. It's seriously a bizarre mashup, but holy hell does it ever work. In fact I'd go so far as to say this is probably the best vampire movie ever made, with a bar scene that holds out as one of the most uncomfortable and absorbing scenes I've ever witnessed.
Strange Days
Another Kathryn Bigelow movie, but this time set in the last days of the 20th century in a cyber punkish Los Angeles. Written by James Cameron, it is easily one of my favorite sci-fi movies and has some amazing chemistry between the two leads (Ralph Fiennes and Angela Bassett), both of whom are some of the best written and developed characters I've come across in the genre. I was actually watching this on New Years Eve with my girlfriend and some of her friends and it was amazing how much of the movie is still relevant to this day and age, despite being set 13-years in the past, and being made in the mid '90's.
Dark City
Neo-noir sci-fi movie that many people sarcastically refer to as The Matrix before The Matrix. Honestly that comparison is a little pretentious as the two movies are very different from each other, while still sharing a common thread of "what is reality", which was a common story trope in the '90's as things like the internet and computers were still pretty new to people. If you're into art deco architecture, this movie will make you very happy, with some amazing sets.
Brotherhood of the Wolf
2001 French action movie that also manages to be a period piece, a horror movie, a romance movie, mystery thriller, and a kung-fu film all at the same time. That may sound a little schizophrenic, but it actually manages to pull it off surprisingly well. You also get to see Monica Bellucci's boobs, so that really should be reason enough.
Videodrome
My personal favorite David Cronenberg movie, largely because it stars James Woods, who's one of my favorite actors. Cronenberg really goes all out in terms of body-horror in this one, and there are a lot of really surreal scenes that you will remember and want to talk about later.
C.H.U.D.
This is kind of lampooned as a joke movie, but I think that more comes from the acronym of the title (Cannibalistic Humanoid Underground Dwellers), but I think the movie has a lot more to say about the plight of the homeless and urban decay than people give it credit for. Moviebob kind of touched on this idea in his review of Hobo With a Shotgun, with low budget '80's movies being the antithesis to the Reagan-era mentality.
I think that's enough for now, but I did try to make sure my recommendations were available on Instant Netflix.