Permanent Arcane Sight. The user can see magical auras by sight without having to concentrate and can still determine magical schools, etc with a succesful Spellcraft check.
Especially in D&D, there is SO much that can be magical: Magic items, spells on a character, magical traps, magical wards, illusions, charms, weird magic fountains, enchanted archways, wish-giving rocks, etc. The problem is not having to keep track of all the magic stuff, but having a PC with an ability that automatically detects magic traps, illusions, a charmed NPC, magical wards, weird magical effects and so on. It is hard to keep anything from someone with permanent Arcane Sight because the game is so magic heavy. AND having to keep telling the player EVERYTHING that is magical AND what the strength the aura is AND what school, and so on. When the party encounters some enemy NPCs the Arcane Sighted Wizard wants to know: what auras are on each NPC, where are the auras, what strentht are the auras and what school? It's a pain in the butt for a DM. So, in my "roll"-playing campaign, more and more NPCs and objects are getting Nystals Magic Aura or Non-detection on them
Polymorph-type spells can be a nuisance because they can beef up a single character in multiple ways all with one spell. But that usually just means I can send tougher opponents at the PCs.
Insta-travel spells like Dim Door and Teleport I dont have a problem with usually.
Anti-affliction spells are what I tend to find annoying. How bad is a curse when Remove Curse gets rid of it? How bad is a disease when Remove Disease or a Paladin's ability gets rid of it? Basically, the party does not suffer a detriment for very long because there are spells or magic that will end the effect instantly.
B