Boy, this is a tough question as it is very subjective. Well - let's see, let's start with LOCATION. The best locations in South Beach / Mission Bay really are going to partly depend on individual preferences, but I think most people will agree the Delancey St / Brannan intersection is probably one of the most popular locations to live - right there you have The Brannan, Jenn Davis's 200 Brannan, and OW (Oriental Warehouse), as well as other buildings nearby (1 Federal, Cape Horn Lofts, 301 Bryant and some buildings nearby).
Mission Bay, you really only have Berry St in my opinion and over there you have 255 Berry, 235 Berry, Arterra, Park Terrace.... 4th and King/Townsend is a very CONVENIENT location for public transportation and everyday shopping (Safeway, Borders, Walgreens all nearby), 3rd and King/Townsend is also bustling and convenient too in Mission Bay but not exactly quiet and can get busy during ball games - so I do not know what you mean by GOOD LOCATION - do you mean, active, alive? Do you mean, quiet/serene? What do you mean by good location?
Other locations in South Beach that are "good" are the intersections of Main and Folsom - 1 block from the Embarcadero and waterfront - The Infinity (my personal favorite!) is located right there as well as 300 Beale (Embarcadero Lofts) nearby as well as 75 Folsom St. Honorable mention for great locations in South Beach would include the area around South Park on 2nd St.
Quality buildings I think you have to start with The Brannan, hands down the best built/quality building in this area. The Infinity is good too - 200 Brannan, 300 Beale St (Embarcadero Lofts) is a quality loft conversion building, Watermark is considered to be a building of reasonable quality too - 301 Bryant is also highly regarded. There are just so many good buildings to be honest.
HOA fees - I assume you don't just mean, HIGH HOA fees, but HOA fees that are a good value, The Infinity gives good value for the HOA fees I think for a full service / full amenity building. If you are looking for low HOA fees then you should turn towards some buildings on Berry St in Mission Bay like 235 Berry and 255 Berry for example.