1. HashCows - if they can get their pool back up to the rates and power they had before the hack, they're in contention. Right now they're woefully underpowered (my sentiments and assessment of their current state of affairs have been agreed to by their admins Atriz and NearMiss).
2. Wafflepool - I've evaluated them 3 times, and each time it totally underperformed MC over the course of a week. They rely heavily on autotrading, so they'll need to get their hands dirty with manual trading if they hope to compete. Still, they have a good infrastructure and site setup so far.
3. ScryptGuild - Eleuthuria of BTCGuild has this as a new pet project and it's currently in Alpha with partial features. He's planning on a public beta soon. He will eventually have auto-trade and conversion to BTC, but this is not active yet. Right now it's more like Multi-pool, but it will eventually resemble Hashcows in capability (options to either keep coins or trade to BTC) with the added capability to keep mining your specific controlled set of coins or let it Auto-jump to most profitable (like MC and Hashcows now). I haven't seen this one talked much about here, but it has one of the biggest BTC Pool masterminds behind it and as such will probably have the strongest backend infrastructure which will be shared with the huge and powerful BTCGuild. One to watch.
I'll be keeping an eye on all of these, and other smaller pools mentioned here, but for now Middlecoin is still the most profitable I've seen.
There is also clevermining.com
Yeah I haven't evaluated them and they're brand spanking new, so didn't want to render an unqualified opinion on them yet. We'll see how they do long term.
And also trademybit.com - I split my hashpower between MC and trademybit for last two weeks and reslts are quite similar in long term (to be honest most multipools mine DOGE most of the time, so no surprise). But above all, TMB have a fancy web, bit confusing stats and nice graphs