AnimeNewsNetwork's only been mentioned once in passing, so it deserves a little more attention:
Pros:
Relatively easy to add titles, either from individual anime pages or alphabetical lists.
Rating is fast and easy once titles are added
Allows customized lists
Best-formatted comment/mini-review feature I've seen.
Allows several sorting options, including by comment
Can track manga, database is reasonably complete aside from some very obscure titles
Can view entire list on 1 page if desired, or customize items per page
Tracking of DVD collections
Can find the lists of "like-minded" users to assist in the search for recommendations.
Cons:
Can take awhile to add anime, unless you go by the alphabetical lists
No default "stalled" or "Won't Watch" / blacklisted categories
No fansubber or ripper info
No episode progress or total time watched tracking
No language options for title sorting, i.e. you'll find Strawberry Marshmallow / Ichigo Mashimaro in "S" no matter what.
No tracking of start/end dates.
Anime-Planet is very easy and fast for adding and rating titles, but the database isn't complete (hentai effing where?), doesn't track rewatches, and doesn't track any information on viewing formats, legal or illegal. Tracks total time watched and allows some customization. No tracking of start/end dates. Tracks manga (I think?)
MyAnimeList: interface isn't hard to use, but adding and rating titles is very slow and cumbersome. I can say that I never would've maintained an MAL list if I hadn't been able to import my AniDB list to it. Even then, I had to go find every random little omake, sidestory, and unaired episode that MAL has separate entries for, like
this one. Tracks DVD collection and fansubber/ripper info, but only vaguely. (You have to remember or guess how many GB a series occupies, for instance.) Tracks rewatches and started/finished dates. Shared anime list with rating comparisons is a good feature, although I use it more for giving recs than getting them. No language sorting options, which is especially annoying because they randomly use English titles for some shows and romaji ones for others, irrespective of licensing status. Also tracks manga, though I don't use that feature.
AniDB: Although I'm an old-time ANN loyalist, I have to say AniDB is my overall favorite. Very complete database, tracks rewatches, episode progress, start/finish dates, release groups, file size/type/quality, time spent, total file size, and legit-media watching. I've seen a lot of complaints about AniDB being confusing or user-unfriendly. However, I've never felt that, even when I was new to downloading anime back in 2005. Adding and rating is fairly quick and easy. I add everything manually, although I understand there are programs that can automate the process. AniDB's list sorting can't be beat: user-review ratings, overall site ratings, airdate, progress, total series length, you name it. And then there's the filters, which allow you to answer questions like "what're the top-rated anime in my list that I haven't seen yet?" And then there's the integration with the tag system, which allows you to find more shows with your favorite
fetish elements story components that you haven't seen.
So since they all have their pros and cons, I use them all. That way, there's less of a chance that some show will slip through the cracks of my memory and not get added.