Just my opinion, but Civ III Conquests was a better game than Civ IV vanilla. Only with BTS and fan-generated content has IV become worthwhile.
This has been my general stance as well. I played Civ 3 all through time of Civ 4 and warlords and a few months after BTS's release. When I finally got BTS and installed Bhruic's unnofficial patch, I have yet to go back to 3. And I honestly do not see a reason to.
OT would still have a bias. Generally a bias towards Civ 2 or 3. That's because OT mainly consists of people who don't play Civ anymore, so are less likely to like the more recent version. One OT poll I could find was 6 votes a piece for Civ 3 and Civ 4, which, IMO, shows a Civ 3 bias (seeing as Civ 4 is clearly better, yet Civ 3 got equal votes).
I am just quoting this because it made me laugh due to the bolded part.

But I agree OT tends to favor 2 and 3 for the reasons Camikaze states.
Civ4 is a vast improvement over Civ3 which was a vast improvement over Civ2 which was a vast improvement over Civ1.
Now I am gonna use this post as this is how I feel about the series as well. Each incarnation of civ has improved upon itself and I love that Civ is not a game that is afraid to try new ideas. Civ 1 was awesome, and 2 took things further bringing in those annoyingly tedious caravans that we all probably abused the hell out of. New governments came in, the wonder movies, a much better interface, unique styles to civs outside of color, etc. Civ 2 brought in new fresh ideas to the original game.
When Civ 3 came out, I really don't understand the malice towards it in the fanbase. It brought in natural borders through the idea of culture, additionally a cultural victory. Also bringing in a diplomatic victory. Civ 3 was the first time the AI was not destined to team up against the human towards the end of the game. As in 1 and 2 you victory was conquest, space, or time. 3 brought in the idea of ending the game peacefully through culture and diplomacy. Also they brought in the idea of military resources. They tried something new with artillery that I liked but needed some fine tuning. They also brought in the idea of the worker unit, great people, wood chopping creating yeilds, leader traits, probably some things I aint remembering. At any rate 3 was the most inovative addition to the series and had a much bolder approach as a sequel than 2.
But it had also taken the ideas brought from 2 and expanded upon them. They took the unique styles to civs in 2 and expanded them into unique units as well as the unique look. Tossed some governments out threw some new ones in for testing. Then they also tested the fanbase for multiplayer to boot.
Civ 4 has basically went as bold as 3 was with BTS. They have greatly improved the Great People system by actually giving it a system all its own. In the same way you have to balance military, techs, gold, etc. now toss in great people points. They have added a new experience system for units to allow promotions to specialize your troops. They have once again tried a new approach to artillery. Land improvements are more versatile. Religion has been added and can be fun and a pain. Health and happiness makes for a better system than aqueduct = 6-12 population and sewer system = 12+. Cities now have a sort of pseudo-personality. Cities have now became something more unique in their own right outside of namesake. The new maintenace (former corruption) system takes some getting used to. Mostly understanding that a city is only as valuable as the land around it. Previous version of civs, a city in a desert was still valid as it meant an defensive outpost. Now, its a bad idea - its better to just throw a fort there if you need it that bad. Civ 4 has added in a new espionage system, coorperations, vassal relations/colonies (as "minor" civs not a hut mining a resource), etc. Additionally you can now see for the first time WHY a civ is friendly, cautious, or annoyed with you. (Ex: +2 "Our open borders have brought us closer together") This helps you be able to manage your diplomacy.
As for which you should purchase, I would say 4. 4 has all the innovations 3 has plus some and expanded upon them. The game has moved in a positive direction towards offering a wider range of more diverse strategies. Also Civ 4 has really good multiplayer if you are interested in it. Yet another spect they improved this time around.