Fallout 2
Fallout Tactics
Heroes of Might and Magic III
Arcanum

The last one is a toss-up between Commandos Behind Enemylines, HOMM II and Legend Of Grimrock. But it's only for the 5th place so who cares.

Worthy runner-ups: To The Moon, Commandos 2, Painkiller, and Broken Sword. Also, games that might have made the list based on what people have said, but I haven't played yet (but I will): The Witcher and Sacrifice

Does my list count as cheating?

I am stunned it took 14 posts before Ultima VII was mentioned. Credit to you, shame on everyone else.

My top 5:
1. Ultima VII
2. Jagged Alliance 2
3. Deus Ex
4. Fallout 2
5. Space Rangers 2

Thank you good sir, I am just happy to be the first to mention it...though at the same time also sad about that.

Bump b/c of interest. (Only this and the other bump, I promise. ;) EDIT: In hindsight I lied.

Classic

Another World
Broken Sword: The Shadow Of The Templars
Gabriel Knight: Sins Of The Fathers
The Journeyman Project 2: Buried In Time
Lands Of Lore: The Throne Of Chaos

Indie

Gemini Rue
La-Mulana
Legend Of Grimrock
Resonance
To The Moon

The Witcher 2
Pharaoh
Earthworm Jim 1-2
Heroes III
Alan Wake

Age of Wonder
The Book of Unwritten Tales
BG 2
Witcher 2
Sid Meier's Alpha Centauri

Fallout series
Arcanum
Warlords Battlecry III
Sacred Gold
Temple of Elemental Evil

I wonder why this hasn't "taken off". :P

Psychonauts
Alpha Centauri
Painkiller
Unreal
Nox

Classic
Ultima 7 part 1+2
Wing Commander 3
Blake Stone Aliens of Gold
Populous 2: Trial of the Olympian gods
Dungeon Keeper 2

honrable mentions too: Duke Nukem 1+2, Masters of Magic, Thief 2, Syndicate and MDK

Current/Indie
La-Mulana
Primordia
Geneforge 1-5
Resonance
Gemini Rue

These are just a few of my all-time favourites which i am now playing through again.

I really couldn't pick only 5 titles as there are just too many. Top 20 maybe.

Deus ex
freespace 2
fallout 2
outcast
syndicate

Choosing just 5 is VERY hard. GOG has built a nice catalog.

HoMM V
Arx Fatalis
The Witcher 1
Wing Commander Privateer
Master of Orion 1

In no particular order

1. Mutant Mudds
2. Gemini Rue
3. Fallout
4. Master of Orion
5. FTL

I needed one to bump.