The Power Plant dungeon has all sorts of this. The viruses are tough, Mega's healing abilities are crippled, and there are dozens of broken Programs that attack you and behave as viruses. Remember, Programs are sentient beings, so breaking them results in a clearly unpleasant Face Monster Turn.
It should be noted that one of the first ones you meet denies being "altered", which suggests that some asshole (ElecMan, most likely) has been tampering with them and has turned them into mind-broken suicide machines. And the worst thing is, unless you have the ability to escape combat, you're going to need to destroy each one you come across, because broken programs are some of the most dangerous viruses in the dungeon, continually encroaching on your area and brandishing powerful electric shocks. These poor guys are essentially victims of Mind Rape that Mega has to Mercy Kill. What Do You Mean, It's for Kids??!
Lan and Mega entering Yum Square. For reference, Yumland (read: Cyber-India) is supposed to have the world's largest population of NetNavis. As they travel through Yumland's Cyberworld, Lan and Mega are confronted by a notable lack of this population, which becomes painfully obvious when they come to the Square, which is desolate and silent. Mega must walk, alone, through the creepy emptiness, past unattended store counters, following the sound of clicking and clattering, where they find the sole surviving NetNavi who informs them that his entire population has just been murdered.
It gets a whole lot creepier when you're forced to break into the desolated area's vault in order for Mega to achieve Style Change, triggering the security system that keeps attacking you as you make your way to the exit. You're technically robbing the website of the last thing it had.
The scene where Mamoru nearly dies as a result of a WWW attack on a hospital to steal vital data is pretty nightmarish in a mundane way.
Nebula Grey from 5.
CircusMan in Battle Network 6, who is literally a life-stealing Monster Clown. He has an attack that the fanbase infamously nicknames as the "Tent Rape Attack". If that isn't bad enough, the first time you see him, you witness him opening his chest to reveal a vacuum, which he uses to absorb and capture one of the two Cybeasts. If that still isn't enough for you, he also successfully uses it on MegaMan later! He's basically Kirby, without the power transformation part and hundreds of times creepier.
Battle Network 3: the attack on Sci Lab. Frankly, it's one of the more realistic depictions of both hacking and terrorism in the series, which makes it particularly nasty, but the fact that YOU enabled this is probably the worst part.