Not sure on how to decide a favorite, however I just finished watching Full Metal Alchemist and loved it. The follow up movie I didn't care too much for but it gave it some closure.

Now I am looking forward to watching FMA: Brotherhood since I hear it is better since it follows the Manga properly.

Dragon Ball Z
Pokemon

Yeah, not huge on Anime :P

It significantly alters a few of the basic world-rules laid out in the original FMA anime. While the Philosopher's Stone was impossibly elusive in the original anime, it is more attainable in Brotherhood, humunculi are no longer the result of failed human transmutations (won't say what they are, hope this isn't too bad of spoilage), Rose has only an insignificant role, and Dante does not exist

I absolutely love Mirai Nikki. It and Fate/Zero are my clear favorites this season.

Funny thing is Mirai Nikki is almost 100% like Deadman Wonderland, both main males are whiny bitches, both females are yanderes and crazy people make up the rest of the cast, yet unlike DW I don't hate MN infact I love it. Maybe it comes from the fact that Yuna is the most amazing Yandere I've seen in a long time who just makes me laugh then you add in the 9th( Can't remember her name) it keeps me entertained. Now if only they kept the 12th in it longer he was amazing and kept me laughing until the very end.

But female lead in Deadman wasn't too yandere. Just a deadly person with a whimsical, childish personality.

Can you name a few of these series? It seems like every anime I have watched since Ghost has just been a major step down in quality (aside from Ergo like I said).

In regards to Ergo Proxy's popularity, I am just going off of my personal experience as it seems that everyone I talk to (I talk to people about anime on a semi-consistent basis, and I have gone to several different anime cons in my area) have never seen the series or, in many cases, have never even heard of it. This is the first time I have seen anyone refer to it as "incredibly popular." I will not argue against it as it certainly deserves to be popular, and it may just be one of those things where it is just not big where I live.

Cowboy bebop without a doubt. I'm actually getting the last line of the show as a tattoo up my arm next month. "Your gonna carry that weight". That quote really struck me to the core to be honest. I also really enjoyed Claymore and Fruits Basket :).

For ergo Proxy, I've heard countless people name it among their favorites and high on recommendations list. It's also the #65 most popular anime in MyAnimeList's database. I know this isn't the best way to gauge popularity, but this site has a giant userbase (over 200k) and it usually pretty reflective of anime fans.

As far as the shows I mentioned earlier, I must ask for some clarification. Is there a certain genre that you're looking for? I need to know if the content of some would or would not sit well (whether or not to recommend things like Kuragehime, Nodame, or Usagi Drop for example. These are all great shows but they're targeting women rather than men) with you.

I tend to go for stuff that is more philosophical and cerebral in nature. Unfortunately, it seems most anime (at least what I have seen having viewed about 30+ series now) steers away from this in favor of high school romance, comedy, generic action, and countless portrayals of women as objects of lust and perversion (not that I am saying romance/comedy/action/sex are innately bad it is just that they are always handled so poorly as to drag down otherwise interesting shows). 

I don't know if that helps to narrow things down at all. Obviously, sci-fi and anything cyberpunk are a huge plus for me. I am not familiar with any animes that have attempted it, but I also like horror. Also, unhappy endings/sad stories or at least ones with ambiguous endings tend to be my favorites in other mediums.