This includes TBS like the Total War series.

Anyway, mine are:

Age of Mythology
Battle for Middle-Earth II
Supreme Commander

Those three all tie.   Two others are:

Company of Heroes
Shogun: Total War (I sadly haven't gotten any of the later ones.  Samurai ftw!)

RTS I dislike:

Empire Earth (Spending an hour building up a 100 man army only to have it slaughtered in under a minute ftl!)
Warcraft III (It's popularity astounds me, seeing as there are so many other, better RTSes out there.  It's okay in and of itself, but horribly overrated.)

RTS I own:

Age of Empires II + Exp.
Age of Mythology + Exp.
Age of Empires III
Shogun: Total War + Exp.
LotR: Battle for Middle-Earth
LotR: Battle for Middle-Earth II + Exp.
C&C: Red Alert
C&C: Red Alert Retaliation (for PS1)
C&C: Tiberian Sun
C&C: Red Alert 2
C&C: Generals + Exp. (ruined the C&C name)
Company of Heroes
Supreme Commander
Warcraft III + Exp.
Empire Earth II

And probably a few others I've forgotten. 

Starcraft

Age of Empires 2 The Conquerors

Warcraft 3 The Frozen Throne 

 How is warcraft III horibbly overrated?  It is the best RTS out there, hands down.  Either WC3 or Starcraft.  It's almost to a point that these are facts, and not even opinion.

Company of Heroes is great.  I'd put that up near the top.  Command and Conquer tiberian dawn and C and C Red Alert 1 were great.  Red Alert 2 was pretty good too.

If you like Supreme commander, you should try total annihilation.  That was a great game.  It was basically SupCom's predecessor.

and again, how is WC3 overrated? 

I'm a big fan of AoE3, i hated WC3.

StarCraft
Age of empires 2
Warcraft 3 Frozen Throne
Rome Total War

I personaly don't like WCIII because it has too much RPG in it. You have to build your first hero ASAP, and if you don't spend every moment possible ranking him up, you're screwed. I'd always lose battles just because my heroes were 1-2 levels behind my opponents. It didn't matter how much I built, or how good my econ was, because the pop caps were so low that it was hard to maintain a sizeable enough army to counter strong heroes. THe fact that units took a bit long to build made it harder to come back after a rough attack. Sure, other games like BFME had heroes, but they didn't dominate the battlefield because you could rank up your regular units as well, and a strong army could counter a strong hero.  In WC, everything revolved around the heros.  I play RTS to fight wars, not run around killing creeps and collecting tomes.

As for it being horribly overrated, most of my friends, the few others that play RTS, only play WCIII, quite often because that is the only RTS they have ever played, and they usually play RPG custom maps. It would bug me to no end. They'd go, "Wanna play some RTS?"

"Yeah sure!" (getting all excited because nobody ever wants to play RTS)

"Okay, let's play WC3."

Then they'd join an RPG custom map and I'd just quit. Sure there were some fun custom maps like Footmen Frenzy (somewhat similar to Mythodea in AoM, which was a blast), but my friends never wanted to play those.

I'll give you Starcraft being one of the best RTS' ever. There weren't any heroes to dominate the gameplay.

And yeah, I've played TA a few times. Good stuff.

I'm convinced that Blizzard focused so heavily on RPG gameplay elements in WCIII just to breed an install base for WoW. They knew they couldn't compete with the already established fanbases of games like Asheron's Call and Everquest, so they created their own, out of their WC/SC fanbase. 

My top list would look something like this, I only included games that I currently own or plan to own in the near future:
1. Company of Heroes
2. Warhammmer 40K: Dawn of War Diamond Edition (includes the original game and the two expansions)
3. Warcraft 3
4. Homeworld 1
5. Homeworld 2

1. StarCraft (nothing come close beating this monster, this is the best and most balanced RTS ever made)
2. Warcraft 3
3. nothing else come close to those two
4. same as #3
5. same as #3

I played alot of RTS games but I dont think AOE and C&C deserved in the same league as those two. both of those franchise is average at best.

 Have you actually played WC3 online?  I very rarely reach the population cap...  If your hero is 2 levels below your enemies, then you're obviously doing something wrong...  They are creeping stuff while you are sitting in your base for no reason.  You should be creeping as well (and teching), or rushing to attack their base while it is empty (since they are creeping, and will have wounded soldiers and/or a hero with no mana when they run/teleport back to their base).

Of course Heroes are an integral part of the gameplay, but they are no where near as "overpowerd" as you make them out to be.  Heroes are what make Wc3 so interesting.  They introduced such a novel concept into RTS and it worked out so well.  There are too many specific cases to bring up, but there are always counters to other heros.

 You can definantly counter heros before reaching the population cap (again, the game should be over before you can even concievablly hit the cap).  Creeping only gets you to a max level of 5.  If you even let someone creep to level 5, then you are terrible.

Basically, it comes down to this - just because you lack skill or understanding at the game, it doesn't make it bad.  Heroes, of course, are more powerful than other units, but they surely aren't overpowered.  Every strategy can be countered.  If you just don't like the RPG elements fused with the RTS elements, that's fine, I can respect that opinion, as long as you can respect that Blizzard did try something creative and novel with the RTS genre, even if you don't like it.  But to say that the game is overrated because you don't understand it's mechanics... I can't respect your opinion.

And yeah, I'm sorry your friends play custom maps...  There are some good ones, like Footywars, and even wintermaul wars is fun, but I find ladder play to be much more fun than the custom games.