Well it all depends on your taste of genre, tone and the like, since the different comic lines tend to be pretty diverse even within what would at first glance be pretty mono tonal franchises (though New 52 DC has become pretty mono tonal as a whole lately). I could say "start anywhere and see what clicks", but that would be too vauge.
Since you seem to like the MCU (and by your comment I'd also assume Agents of Shield), I'd recommend Secret Avengers. The current line follows Agent Coulson, Nick Fury Jr and a few heroes working for Shield. It's a spy thriller series which deals with their work for shield under secrecy and out of the public eye.
Something to remember for any comic, though, is that unless it's a 6-12 part miniseries there's really no need to start at the first issue. Marvel recently started or restarted a lot of lines, so it shouldn't be too hard to find Issue #1's of current series, but even then a good 90% of all comics aren't that big of a deal if you start at issue 5 or 20 or 163, since almost all of the story tends to be self contained. The other 10% tend to be miniseries, lone series set in their own little world or crossover events.
