Gen I: Rock Tunnel
Gen II: Ice Path
Gen III: Sky Pillar, Route 113
Gen IV: Foggy areas
In General: Surf areas
Rock Tunnel
Basically, you need Flash to get through. And it's not an easy cave, like Dewford Cave, which you can finish without Flash, it's really hard. And long. And all the annoying Geoududes and Onixes and Machops keep appearing and attacking you. Once I went in there to search for a Cubone for my Ground-type team, and it just wouldn't appear. I don't even know if you can find Cubones in Rock Tunnel, but that doesn't make it less annoying.
Ice Path
This was like the most annoying thing EVER. When G/S were new I just never got past it. I was so frustrated, and I hated it! When I bought my friend's Crystal a while ago and came to the frozen hell, I didn't find it very hard, actually I thought it was quite fun. But I remember being sooo worried about not making it. But it went fine.
Sky Pillar
I've never completed Sky Pillar. I just can't control the mach bike, and I hate the place. I'm not going to waste any more words on something as horrible as that.
Route 113
I just didn't like all the soot. It just felt so eerie. And when I looked for Skarmory I never found it. That was just so annoying. And took a lot of time.
Foggy Areas
Basically the same reason as Flash-areas, only this annoyed me especially much. I don't even know why. I just hated them.
Surf Areas
The reasons have been said quite a few times already... Though I like them in ONE way, as I found my shiny Tentacool while surfing. It is now a shiny Tentacruel and is my surfer in Sapphire.