I've been looking hard at all these cars since last year summer:
550i vs 535i
The E60 550i is a waste of money compared to the E60 535i.
With the 550i you get worse MPGs and only 60 more HP than a comparable 535i. A 535i with the M Sport Areo kit and M5 rims look like a 550i. In fact, most reviews on the E60 550i pretty much said to skip it's 360 HP engine and either get the just as sporty 535i at 300 HP or the M5 at 500 HP.
Your BEST bet is to land a 2008 535i Sport Package
(don't get the xi unless you really really need it). You can still find these cars fully loaded with under 50k on the odometer for around $28,000 to $30,000.
E90 335i vs E46 330i
BMW has made the 335i, and all 3 series since 11/2009, more spartan than before. The average E90 335i will be more technologically advanced to an E46 330i but gone are lots of luxury features like proper padded seats, HK surround sound option, ashtray, proper cup holders, seat pockets, foot well lamps, glove box flashlight and charger, etc... The 2008 335i still has the horribly effeminate daily-driver Bangle design and the 2010 - 2011 335i have recall issues with the fuel pump and engine fuel line failure - even if you get one that is trouble free it will in the long term put a dent in resale value and a HUGE cloud over the car's post-warranty reliabilty (see under E46 subframe issue for a great historical example).
Your BEST bet is to land a 2009 335i
(stay away from the xi and the d models unless you really need it). You can get one with less than 30k on the odometer for around $30,000.