Just asking this question out of curiosity because well since GOG does not have the big ones like Warcraft/Starcraft, Dawn of War, Total War games, Command and Conquer, Age of Empire, etc.

So what does GOG have that is the best RTS games?

Well they do have Total Annihilation, one of the best strategy games ever made, you might start there.

Lords of the Realm 2 is a pretty good RTS game, but the real-time part only occurs during battles. Total Annihilation is a good sci-fi RTS game with mechs. Empire Earth is another popular RTS game that's similar to Age of Empires.

You also might want to look into the Anno series. Anno 1404 and 1701 are a lot of fun!

Total Annihalation, Total Annihalation Kingdoms, Celtic Kings: Rage of War, 8-bit Armies, Empire Earth 1+2, Stronghold HD + Crusader, Perimeter + Emperor's Testament, Cossacks Anthology, Knights and Merchants, Earth 2140-2160, Battle Realms, KKND 1+2, American Conquest, AI War, Star Ruler 2, Heroes of Annihilalated Empires, Sins of a Solar Empire, Impossible Creatures, Dungeons 2, Darkest Hour, Meridian: New World, Stronghold Crusader 2, Warrior Kings and Battles. Act of War. There are more there if you like bigger crossgenre mixing.

If you like Total War games you have: Imperial Glory or Dragon Commander

Newer games that are pure RTS: 8-bit Armies! Ashes of the Singularity

Edit: Star Wars Galactic Battlegrounds as mentioned by Hunch. Essentially Age of Empires in Star Wars setting.

Sticking to RTS games in the more classic sense: realtime basebuilding with resource gathering somehow involved, then these would be my top5 (edit: uhm top7) on gog:

KKND
Difficulty builds up to a fever pitch with the last 1 or 2 missions right before you gain access to snipers/dirty harry's, at which point it becomes much easier. The 2nd is quite fun too, but I prefer the first one.

Dark Reign
Someday I'll get past the 2nd level :P

Act of War
Incredibly satisfying combat, and very cool looking bases, with a straightforward playstyle. Feels a lot like a generals sequel.

Empire Earth. The cheating AI can ruin skirmishes a bit, but there are some incredibly fun campaign levels, and nothing can beat this game at multiplayer.

Popolous: The Beginning\
Light on basebuilding and resource gathering, with a greater focus on combat and micro-ing your shaman. Criminally fun though and utterly timeless. Possibly my favorite Bullfrog game. Well either this or:

Dungeon Keeper
nuff said.

Stronghold
Personally I prefer this one over crusader. It's a pity enemy attacks come so quickly though. It never feels like you have enough time to build a proper castle. At least the scenarios can be used for that.

Moving completely away from the classic RTS game, something totally worth cheching out is Majesty with its unique take on rts warfare. Crazy difficult though, at least the later levels. There are several other good rts games on gog, like those already mentioned, but I've only played the above ones in any detail.

I can vouch for Act of War being pretty cool (Direct Action, at least). The story and acting in the FMV cutscenes are B-grade action thriller trash...but who plays pure RTSes for story, anyway?

I don't think Star Wars: Galactic Battlegrounds has been mentioned yet. I haven't played it, but a lot of people seem to like it. o_O
I have to say, I haven't seen any RTS games like that around here....

Star Wars: Galactic Battlegrounds
Stronghold / Crusader
Dungeon Keeper 2
Populous: The Beginning
Impossible Creatures

Original War (unfortunately no longer available for purchase; Bohemia are poopy-heads)

Haha, good joke :) Fixed my mistake.

I meant games like Spellforce that have RTS elements and rpg elements.

Best RTS on GOG ? thats kind of diificult to tell cause everyone has it's own favorites,
and like you said:
command & conquer classics , red alert classic , are not on GoG, nor are age of empires 1 and 2 , Dune 2000 is not on GoG, and these are the best RTS imho... .

They probably never ever arrive here DRM free now they belong to EA , they are 'milking the cow dry', so it be a cold day in hell, or when hell freezes over or pigs can fly before that will happen , i guess they'ed rather go bankrupt then
release these fabulous games DRM free.

Baldurs Gate is not RTS, KKnd 1+2 are RTS they are okay but not the best , and KKND are buggy as hell (pardon ma french), have graphic artifacts.

Fallout Classic also no RTS .... so it gets pretty hard for me to name the best RTS here at GOG.

Well i almost forgot the wonderfull commandos, the classic games only ofcourse (they are labeld as RTS on GOG ( i just searched for it) cause the games went down hill, and all the way down the drain aswell when they changed the engine from commandos in commandos 2 and 3 (horrible it is) , the latest one is awfull its FPP....

Not played it yet, but AI WAR: FLEET COMMAND looks interesting.

Peremiter is a sequel to the sci-fi racer Vangers. It has voxel based teraforming and is focused on base building. I really like its music and the over-the-top scifi weirdness. However, I got stuck early, so I have to read the manual.

Ground Control 2 is pretty solid too

My vote goes to Stronghold Crusader.

It has a great setting, looks really good, has great challenging gameplay, and is fun in any mode (some games I cannot play in random map some games have lousy campaigns, Crusader does not).

Total Annihilation is fun, but I really like Total Annihilation Kingdoms more. Here it's for the campaign. Looks really good, has good lore, and is just fun.

Earth 2140 is also really fun, but it gets really hard.

Empire at War (especially with Forces of Corruption) and Galactic Battlegrounds are great, with Battlegrounds being more for ground AOE style matches and Empire at War for grand campaign and space battles.

World in Conflict is a slight stretch with Ground Control 1 (didn't get to play enough of II before my computer fried) but it is incredibly good and really fun. More of a tactics game than an RTS but this is what the reviewers called it.

I'm going to assume we're splitting hairs over RTTs and the military style RTS/RTT games. But, finally, what I played of Battle Realms was also good.

KKND looks really good. Last time it was on sale I passed on it, kinda regretting that.

How is Dark Reign*? I was looking at threads about RTS games from the late 90s and it seemed like people mostly fought over Starcraft or Total Annihilation but if there was a third choice it seemed like Dark Spire was it. I fist saw it a little while ago looking at an old Gamespot review of AoE** where they preferred Dark Reign in some ways.

*: was Spire.
**: was 2, but it's the first one.

Pax Imperia 2 - an underrated 4x rts.
Rage of Mages - rpg/rts mix
+ the stuff mentioned by others before.
Imho it's missing Imperium Galactica 2 the most. I mean wtf it's even available on Android, yet not here.

What is this "Dark Spire" you speak of? Perchance did you intend to say Dark Colony?