Hm...well... I have to say I liked both GC:CS and Clicker Heroes(possibly GCCS a little more).
While what xeano321 says is true about "hot", it's kind of an incomplete explanation. Both good and bad things can become "hot"; a "hot" trend is not necessarily bad. Furthermore, good things tend to become more "hot" than bad things - this should be kind of obvious. Quality is causally linked to popularity. A good game is going to be played by everyone at least a single time, just because it's highly rated. There's nothing wrong with that, it's a smart use of your (presumably limited) time.
Now that we've established this point, we can focus a little more on why these games are quality(warning: is quite long).
1. Good devs: Their devs really care. It might not be directly obvious, or relevant, but if you poke around, you can see the hard work they do. This matters. There's been updates, balance fixes, etc.
2. Replay value: There's a lot of content. And not just in a generic boring way. There's unique stuff to do, and you can keep coming back for more.
3. Progression: You feel like your time is spent doing something that matters. In clicker heroes, you get hero souls and ancients. In gemcraft, you get wizard levels and skill points. When you come back to somewhere that you beat, it gets easier, and noticeably so, allowing you to continue pushing on.
4. Anti-grindiness: The games are decently balanced. That is to say, it doesn't feel like a terrible grind fest(ex: must-a-mine, where your minimum run time is 8 hours purely due to animations for cutting through layers). The games might be long, but they don't FEEL long(to most people). The rate of improvement is significant and noticeable.
5. Strategy: There's a sizable element of skill to each game. In CH, if you leave all your souls unspent, or worse, buy crappy ancients, your progress will be slow. In gemcraft, if you don't place your towers or pick your skills well, you can find scenarios fairly difficult. This matters because you get to make decision that matter.
5b. Powers: The abilities in CH, the strike spells in GCCS. Both make a big difference when used carefully. This allows players to cause a sizable impact on the game, without breaking the game.
5c. Randomness: (Not in a bad way). In CH, there's the treasure chests, the candy/ice, the gift packages; in GCCS there's all the flying ones and the special waves. These help break up the monotonous feel, as you can often get ahead if you deal with these.
6. Multi-dimensional: You can advance on multiple fronts, both short-term and long-term. In CH, you can go for new heroes, buy upgrades, or level old heroes to 1k+ in the short term; in the long term you can buy ancients, regild, or stock HS. In gemcraft, you can build towers, trap manafarm, and enhance with amps in the short term; in the long term you can invest in skills, or in talisman fragments/raw xp with shadow cores. This helps in case you get stuck on one of the fronts, there's always more room in another direction.
7. Story: There's a reasonable amount of story. It's not volumes of RPG text like starwish: RPG Shooter(something I recommend) where there's a near book's worth of dialogue, but it's definitely more than: "Here's some monsters, go kill them". It's somewhat less obvious in CH, but if you go and read the upgrades and the buy descriptions, there's quite a bit of story and references to pop culture cleverly hidden within, even if kashoople doesn't think so.
8. Scaling: The games scale pretty well. Sure, you can "break" the game at some point, but for the vast majority of players, things don't get absurdly difficult(ie arcuz 2, where killing the final boss in NG+ takes 3 hours), or absurdly easy
9a. Smooth controls: There's quite a few hotkeys for everything. In CH, you can ctrl, shift, and z click; in GCCS you have all the wonderful hotkeys for combining. The controls aren't jerky, you can pretty easily get where you want. It may not seem like much, but it contributes to the overall game experience(it's kind of related to #1)
9b. Glitch free: (Mostly). I don't recall any gamebreaking ones, and the active devs really help on fixing problems.