The current top 50 of best games is:

Version: 11/10/2011
(previous version: 20/06/2011)

Expansions, adaptations, role-playing and children's games aren't taken into account in this list!
But note that the good expansions/adaptations are mentioned below each game.

Position	Last position	Game	Publisher	Year
1	1		Puerto Rico Alea	2002
2	2		Through The Ages Czech Board Games	2006
3	4		Caylus Ystari Games	2005
4	3		Funkenschlag/ Power Grid/ Hoogspanning 2F- Spiele	2001
		Good expansions: Benelux & Central Europe (Benelux Zentraleuropa) and Die neuen Kraftwerkskarten (Power Grid Power Plant Deck 2)
5	5		Descent: Die Reise ins Dunkel/ Journeys in the dark Fantasy Flight Games, Heidelberger	2005
		Good expansions: Well of Darkness (Quelle der Finsternis), Altar of Despair (Altar der Verzweiflung), The Road to Legend (Wege zum Ruhm), The Tomb of Ice (Gruft aus Eis)
6	6		Die Fürsten von Catan/ The Rivals for Catan Kosmos	2010
		Adaptation of Die Siedler von Catan: Das Kartenspiel (Catan Card game/ Kolonisten Kaartspel)
7	8		El Grande Hans im Glück	1995
		Good expansion: El Grande: Grossinquisitor & Kolonien
8	7		Agricola Lookout Games	2007
		Good expansion: Agricola: Farmers of the Moor/ De Veenboeren/ Die Moorbauern
9	13		7 Wonders Asmodée, Repos Productions	2010
		Good expansion: Leaders
10	10		Euphrat & Tigris Hans im Glück	1997
11	11		Dominion: Intrigue/ Dominion: Die Intrige / Dominion: Intrige Hans im Glück	2009
		Integrates with Dominion (2008), which has several good expansions like Seaside (Hijs de Zeilen) and Prosperity/Blütezeit (Welvaart)
12	9		Yinsh Don & Co	2003
13	15		Der Herr der Ringe: Der Ringkrieg/ War of the Ring Phalanx Games, Fantasy Flight Games	2004
14	12		Die Fürsten von Florenz Alea	2000
15	17		Brass Warfrog	2007
16	14		San Juan/ Puerto Rico Kartenspiel Alea	2004
		Good expansion: New buildings (10 Jahre alea - Schatzkiste)
17	16		Die Säulen der Erde/ De Kathedraal Kosmos	2006
		Good expansion: Expansion for 5-6 players (with extra features)
18	19		Die Burgen von Burgund/ The castles of Burgundy/ Les Châteaux de Bourgogne Alea	2010
19	20		Roads and Boats Splotter Spellen	1999
20	21		Time's Up R&R Games, Asmodée	2000
21	22		Pandemic/ Pandemie Z-Man Games	2008
		Good expansion: Pandemic: On the Brink/ Auf Messers Schneide/ Virus Alarm
22	26		Le Havre Lookout Games	2008
23	18		Java Ravensburger	2000
24	28		Carcassonne Hans im Glück	2000
		Good expansion: Händler und Baumeister/ Builders and Traders/ Kooplieden en Bouwmeesters, Good adaptation: Die Jäger und Sammler/ Hunters and Gatherers/ Jagers en Verzamelaars
25	29		Carabande/ Pitchcar Goldsieber, Ferti	1996
26	27		Troyes Pearl Games	2010
27			Sid Meier's Civilization: The Board Game/ Civilization - Das Brettspiel Heidelberger, Fantasy Flight Games	2010
28	23		Schatten über Camelot/ Shadows over Camelot Days of Wonder	2005
		Good expansion: Merlin's Company (Merlins Macht)
29	25		Goa Hans im Glück	2004
30	34		Im Jahr des Drachen Alea	2007
31	24		Torres FX Games/ Ravensburger	1999
32	33		Dungeon Twister 2: Prison Asmodée	2009
33	35		Fresko/ Fresco Queen Games	2010
34	36		Steam/ Age of Steam: Rails to Riches/ Stoom: Rails, Roem en Rijkdom Phalanx Games, Mayfair Games	2008
		Adaptation of the well-rated Age of Steam game (2002 - Warfrog, Winsome Games, Eagle Games)
35	42		Löwenherz/ Domaine/ Leeuwenhart Goldsieber/ Kosmos	1997
36	37		Space Alert Heidelberger, CGE	2008
37	38		Keythedral R & D-Games, Pro Ludo	2002
38	32		Ohne Furcht und Adel/ Machiavelli/ Citadels Hans Im Glück	2000
		Good expansion: Die Dunklen Lande/ The Dark City/ Donkere landen
39	39		Small World Days of Wonder	2009
40	31		Blokus Sekkoia	2000
		Other good games in the Blokus series: Blokus Duo (for 2 players), Blokus Trigon and Blokus 3D (aka Rumis)
41	30		Imperial 2030 PD-Verlag, Rio Grande Games	2009
		Adaptation of Imperial (Eggert Spiele)
42	48		Stone Age/ L' Âge de Pierre/ Stenen Tijdperk Hans im Glück	2008
43	41		Die Siedler von Catan Kosmos	1995
		Good expansions: Die Städte & Ritter (Steden en Ridders) - Seefahrer (Zeevaarders) - Das Buch zum spielen
44	44		Junta Descartes, West End Games	1985
45	45		Tribun/ Tribune: Primus Inter Pares Heidelberger, Fantasy Flight Games	2007
46	43		Twilight Imperium 3rd Edition Fantasy Flight Games	2004
47	49		Tzaar Don&Co, Smart Games	2007
48	40		Wikinger/ Vikings Hans im Glück	2007
49			Machtspiele/ Power Struggle Eggertspiele	2009
50	50		Medina Hans im Glück	2001