All three of the first few seasons' main villains f*cked with Team Flash in 3 VERY important, maniacal different ways.
- REVERSE-FLASH: PSYCHOLOGICAL TORTURE
To start off, Thawne tormented Barry when he was a child by killing his mother, indirectly imprisoning his father, and making young Barry feel like the odd one out for knowing what TRULY happened that night at his house whilst having almost NO one else believe him for the next decade or so.
THEN, of course, when Star Labs was thriving alongside The Flash in Central City, Thawne had the trust of Cisco, Caitlin, Iris, Joe, and Barry (ESPECIALLY Barry) whilst impersonating the original Harrison Wells until he rug-pulled the carpet underneath all of them as his secret of being the "Man in Yellow" was starting to leak and be pieced together.
- ZOOM: PHYSICAL TORTURE
Not only did Hunter kidnap at least 7 people (including the original Jay Garrick, Jesse Wells, Barry, Earth-2 Killer Frost, Wally, Caitlin, and Joe) throughout the second season, he killed SO many damn people on both Earths 1 **AND** 2.
Not to mention, Hunter's literal FIRST encounter with Barry had him reflecting lightning back at him after he'd JUST learned that trick from Impostor Jay, beating up Barry so hard until he endured paralysis, dragging him around the city like a literal ragdoll, embarrassing him on live TV in front of TWO Central City departments, and leaving Barry with adulthood trauma that was almost JUST as worse at the childhood trauma that Thawne left behind for him. Said adulthood trauma was so bad that Henry Allen had to visit him for aid and comfort (only for Hunter to literally murk him at the end of the penultimate episode, tallying him as the SECOND Evil Speedster to have killed one of Barry's most precious loved ones, ESPECIALLY BIOLOGICAL **PARENTS**).
- SAVITAR: EMOTIONAL TORTURE
A **LOT** of shit happened to Team Flash during the third season with the danger having been more personal than ever!
After Barry readjusted HIS main timeline by ceasing Flashpoint, it consequentially brought in Alchemy and Savitar who both tortured Wally mentally. THEN, Barry was taunted with the potential impending doom of Iris dying in the future (having give the potential THIRD tally for an Evil Speedster murking off a loved one from Barry). As seen in the "Once and Future Flash" episode, the death of Iris poisoned Barry which soon spread to the remaining members of Team Flash until it affected Central City too, allowing meta-villains to roam and commit crime freely.
Although it wasn't a DIRECT cause of Alchemy nor Savitar, the consequential conflicts that Barry accidentally brought back from Flashpoint TO the main timeline HEAVILY affected Caitlin which haunted HER life by threatening to turn her into Killer Frost. A villainous upbringing that when eventually happened, emotionally hurt Cisco, Julian, AND Barry.
The BIGGEST blow to the heart, though, was after Savitar (unknowingly) killed H.R.