I'm using the pubmed RSS feeds : http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/040_060.html

... and ... twitter.

I used to use RSS feeds of PubMed searches. However, there got to be so many alerts that I just ended up hitting "mark as read." That may depend somewhat on the topic.

Like Pierre, I use Twitter. Follow people with similar research interests and they will broadcast publications of interest to you.

Really though, I've given up on the whole idea of alerts. I just run search instead, "as and when" it occurs to me and bookmark whatever catches my eye.

Unsurprisingly, scholar.google.com gives alerts that are eerie in their goodness of fit to your existing publication record. Their site is also useful for citation-counting navel-gazing.

I discovered the Google scholar "updates" functionalities thanks to Jonathan Eisen's blog here: http://phylogenomics.blogspot.com/2012/08/wow-google-scholar-updates-big-step.html and here: http://phylogenomics.blogspot.com/2012/11/quick-post-nice-microbial-genomes.html

And I have to say I like it too!

I subscribe to Table of Contents of selected niche journals (you stumble across interesting papers you would miss otherwise), I rely on Twitter, however I access the stream via Prismatic and Flipboard (they apparently use two different sorting algorithms, which complement each other), plus I monitor bookmarking services (CiteULike, Mendeley, whatever is out there) of a few people relatively far away from my field.

For certain topics, I also check citations of a few key papers in the topic. However, this is not as regular and not as automated as I would like.

CiteUlike Watchlist but also Twitter

I use mendeley, beside it's regular searching capabilities you can join groups about specific topics where people add interesting papers about that particular topic.

http://www.mendeley.com/research-papers/

I like the "My NCBI" tool - it sends me a monthly email, unfortunately PubMed can be a few months behind the actual article. I should probably try Google Scholar to compare. I also read a few blogs.

http://www.ncbi.nlm.nih.gov/sites/myncbi/

Another tool you might consider is https://www.daily-academic.com it lets you create custom feeds based on keywords or journals and aggregates daily papers for those criteria. You can set up multiple feeds (e.g., one for a specific topic and another for particular journals) so you don’t have to manually check each source every day. (Disclosure: I’m the creator, but I built it specifically for researcher workflows like this, and it’s free for now.)

It’s similar in spirit to using RSS + filters, but with a broader set of options and a simple interface.