People ask me all the time which company offers the best DNA test for genealogy research. For Y-DNA, I always recommend FTDNA. For autosomal DNA the answer is....it depends! This article will mainly focus on 23andMe Relative Finder/DNA cousins and FTDNA Family Finder since I can't comment (yet) on Ancestry.com's autosomal DNA because they wont sell it to me because I'm Canadian.
If cost is not a major consideration, and medical results won't distress you (or you can resist unlocking them), I'd advice anyone to test with all 3. At today's prices, you can test at all 3 for less than testing at just one cost me less than 3 years ago.
Testing at all 3 will give you the most matches, and the most tools. If you are adopted or looking for an unknown parent, it is impossible to predict which company a close relative may have tested with. All three have something to offer that the others don't. If you are an avid genealogist, or have a mystery you are hoping to solve with DNA it may make sense to test at all 3 as well.
If you are a more casual genealogist and/or cost is a major consideration and testing at all 3 isnt an option, then you will want to carefully consider which company to test with.
FTDNA recently changed their price for autosomal DNA testing (Family Finder) to $99. This brings it in line with Ancestry.com and 23andMe.
How many matches will you get?
23andMe will give you more matches than FTDNA unless you are from a group such as Ashkenazi Jews who will receive an insane number of matches anywhere. 23andMe has a cap of about 1000 matches. They will only show you the top 1000 matches. Since FTDNA doesnt have this cap, if you are from a group like Ashkenazi Jews, you may get more matches at FTDNA than 23andMe
At FTDNA I have about 475 matches. At 23andMe I have about 2476 matches. Adjust that down by 8 because those 9 are people I tested there, already knowing they were related. So that is 2467 matches. Yes, I know I said they have a cap of 1000 matches, but there are some (limited) ways around this. So, it seems 23andMe wins this one.
It isn't just about how many matches you have. At FTDNA you get the names, and often family trees for your matches. At 23andMe, unless the match is a Public Match, you can't see their names or family trees etc. until they accept a sharing request. I send invites to all my matches and having sharing with 1028 of them. Another 144 are Public Matches. So, I have names on 1172 matches. Again, seems 23andMe wins this one, but I must say sending out all those invites was very time consuming, and it took me over 2 years to establish sharing with that many people.
Raw Data downloads/uploads
Another consideration is if you can download your raw data, to take to other sites like gedmatch.com for use of the tools there. Both FTDNA and 23andMe allow you to download your raw data. FTDNA allows uploads of your raw data from Ancestry and 23andMe. Ancestry and 23andMe do not accept 3rd party uploads at this time. So, if in the future you may want to be at more than one company, you could test at 23andMe now, and upload it to FTDNA later. This may be a special consideration if you aren't testing yourself, and may not have the ability to test the testee in the future (ie an elderly grandparent, etc.)
On a more advanced point, the segment matches are rounded at 23andMe and not rounded at FTDNA. I consider this one of the stronger features of FTDNA. On the flip side, you can not compare segments of matches to each other in Chromosome Browser at FTDNA, but can compare any two people in Family Inheritance: Advanced at 23andMe. For detailed DNA match analysis to find common ancestors this is a major downside.
Only 23andMe gives detailed medical info (currently 23andMe is not giving medical info), so if this is something that interests you then score one point for 23andMe. On the other hand, if medical info would freak you out, score one point for FTDNA. Personally, I'm neutral on the medical info
Both 23andMe and FTDNA's Family Finder have their good and bad points, so I'll stick to my answer: It really does depend....Regardless of which company you choose, you should consider uploading the Gedmatch.com, which allows comparisons to people tested at the other companies with others who have also uploaded their data.
*I'd like to point out that despite the odds being on my best matches being at 23andMe, my three top matches (all closely related) ever discovered thru DNA testing (I knew their names in my family tree, but didnt ask them to test, they tested on their own, and showed up one day on my match list) are all at FTDNA.