Yes, I agree entirely. Search and citation management seem better left separate to me.
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I used to work at an academic library and one of my colleagues put together this comparison chart of some of the options mentioned. Hope it helps:
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I’ve played around with Mendeley and Papers 3 for the past few years. Both Mendeley and Papers 3 have methods for being able to insert citations and automatically format the reference/bibliography page in Word, but I would say Mendeley has a more robust and stable plugin. I haven’t had a chance to test Zotero too much because my university library gives us free storage with Mendeley. Mendeley does have a PDF viewer and markup engine built within to sync highlights and notes, which may be helpful.
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I’m a long term Papers 3 user. I think it gives the best overall experience of finding papers through PubMed etc., displaying and marking-up the PDFs and then managing the whole bibliography end of things. I suspect other software might do the individual components better but Papers seems to give the best overall performance. There is an iOS add with Dropbox syncing which is…OK.
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I think an important aspect of this Q is how easy it is for you to import and export your data. I use BibDesk, but the first 500 or so of the 6000+ refs in my database came from a Paradox database I built on Windows 3.1 (also wrote my own WordPerfect macros to handle adding refs. and generating a bibliography). More than 20 years later I’ve come full circle and built a custom FileMaker Go database to get my refs. on iOS after PocketBib was abandoned. This all took a lot of custom scripting and template building etc., and I’m not sure I’d recommend it.
But if you’re in academia your refs. are going to be with you for a long time, so I’d pay close attention to export formats (and how much customized structure - groups, smart groups & the like) can be exported. BibDesk is nice in this respect b/c between templates and AppleScript you can get everything out of it. Finding a program that can intake it all is tricky — one deterrent to leaving BD is that nothing else I’ve tried can be coerced to import all the data & structure BD can export.
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I use EndNote—The university where I am a professor has a license. Mostly everyone I know and work with it uses Endnote. We have access to Zotero as well, but, at least for us, there are memory limitations.
Hank
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Used Zotero a bit in undergrad and it worked amazingly for me all throughout law school. Tried Mendeley and Endnotes and just couldn’t make them function the way I wanted them to.
I use EndNote because when I started my PhD program it was pretty much the only game in town. Fast forward 15 years and given the size of my library and the number of annotated articles it’s storing for me, EndNote owns me despite my finding it incredibly unintuitive and visually unpleasing. One good thing is I’ve had great luck with their customer support. Other than that, I occasionally dream of biting the bullet and changing.
If you like Zotero I would stick with it.
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Interesting, the university I work for has had quite a few issues with support - though my biggest worry is it always seems to take them quite a while to support the latest macOS so installing it in the first 6 months after release can be very tricky.
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One general word of caution: With many referencing software solutions, there is some sort of “point of no return”. Once you are heavily invested in one of them, e.g. once you have built a citation style that fits your needs, it does not make sense to switch…
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I use Mendeley, and it has has a plug in for Word that works pretty well (though every now and then they change something and it all breaks for a while). I hear good things about Zotero, Papers was a top choice among academics I know but I am not sure everyone was entirely happy with the transition to Papers2 and Papers3.
Your question really comes down to two parts:
What system do you want to keep papers referenced ? (and here it is probably Mendeley, Zotero or Papers)
How do you want to cite them in a document without having to do anything manually ?
One thing you might want to think about is your life beyond the MSc, where you may be using another text editor of choice (e.g. wrangling markdown …) some of which have particular plugins for searching different systems.
You can always export to the BibTex file and then get Pandoc to reference that (in fact it is usually easier to have a general BibTex file which you update from Zotero, Mendeley, etc, and then have a standard Pandoc command that has the formatting you want and always looks to the same BibTex file).
That should read… For Markdown you can always export the BibTex file …
I second that. Pandoc is an amazing, versatile tool. Kieran Healy has a lot of useful resources on plain text and pandoc in social sciences.
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I brought this up on another forum after Papersapp appears to be deserted, at least temporarily after their Readcube merger. Heard good things about Bookends, so that might be worth a look… I fiddled with Zotero but somehow never got the hang of the interface, sadly - although I really like that there is so much community support around it and that it’s come a long way since it’s Firefox extension days (if I recall correctly!) 
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I’m late to the party here, it seems. Whatever works for you is great!
One thing to be aware of with Mendeley, in case it matters to you: Mendeley’s owned by Elsevier. My Twitter feed pretty much blew up when that sale went through five years ago.
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Hi, just a fly on the wall here, but a very curious fly… what is the implication of Elsevier having purchased Mendeley? Is Elsevier in turn owned by Koch Industries or something? 
Ooh, Bookends looks interesting, thanks for the link! I use Papers, but it’s rather crash-prone in recent times. Bookends looks like it has all the features I’ve come to rely on, and imports from Papers libraries…
In significant chunks of the academic world — especially those sympathetic toward the idea of open access — Elsevier are thought of as bad actors, and highly predatory (excessive journal costs, plus excessive profit margins).
There’s a really lengthy blog post on it here. Thousands of researchers have pledged to boycott Elsevier at The Cost of Knowledge, and Science published a post with more information here.
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Just a little plug for Bookends again.
This thread over at the Bookends forum, sees a user make reference on 1 July 2018 to a very useful Alfred worklfow that was developed by a fellow-user. By 7 July 2018, the developer invites users to sign up to test a modified version of the workflow, now being built-in to Bookends…
Don’t think there are many referencing products out there that could see something similar happening, never mind at this speed!