Two part answer.
AncestryDNA uses base pairs to determine matches and FTDNA and 23andMe use cM (centiMorgans) for matching. This can lead to matching differences. I believe 23andMe and FTDNA use different minimums for cutoffs which can lead to some matching differences. Overall, these matching differences probably won't be a big deal for matches of close kin. You will probably not catch some more distant matches due to the differences. A good solution here is to use GEDMatch.com. Upload your results there and you can use their standard matching criteria or raise or lower it.
For the most part, your close family should show up on any of the tests. There are occasions when a person may not match a first cousin because they inherited significantly different parts of the relative's DNA.
My reliability comment was directed more towards ethnic or ancestral origins percentages and not family tree related.
Judy G. Russell summed it up best in this blog article:
http://www.legalgenealogist.com/blog/2013/10/27/those-pesky-percentages/
AncestryDNA has rolled out its new ethnicity estimates to its full database over the past month and — more than anything else — the results seem to be underscoring the reasons why The Legal Genealogist has one thing to say about these deep ancestral percentages:
Forget them.
They’re cocktail party conversation pieces — and little more. The science just isn’t there yet to back them up.
While she was talking specifically about AncestryDNA's new results, the comments apply to the other companies and various admixture tools as well.
It's also important to understand that our paper trail DNA percentages aren't necessarily the true percentages we actually inherited.
Kelly did a good job of creating a beginner's guide. Lesson 7 shows how a person's actual DNA might differ from their paper trail version.
https://sites.google.com/site/wheatonsurname/beginners-guide-to-genetic-genealogy
Below are my ethnic/ancestral origins results from the five companies I tested with. I am including the pre and post update for AncestryDNA. FTDNA and 23andMe are working on updates so it should be interesting to see how those changes play out. I have played with most of the admixture tools on GEDMatch and those can show major differences.
To confuse matters, different testing companies and admixture tools may not define regions/areas the same way. Mediterranean may include one set of countries with company A, but a different set with company B.
Family Tree DNA
Continent (Subcontinent) - Population - Percentage (Margin of error ±13.95%)
Europe (Western European) - French, Orcadian, Spanish 80.72%
Europe - Tuscan, Finnish, Romanian, Russian 19.28%
23andMe Standard Comp.
Y-DNA J1e (appears to be the same as FTDNA's J1c3); mtDNA C1b2
98.9% European
Northern European
11.3% British and Irish
6.1% French and German
62.1% Nonspecific Northern European
0.1% Ashkenazi
19.4% Nonspecific European
0.9% East Asian & Native American
0.9% Native American
0.2% Unassigned
2.8% Neanderthal
23andMe Speculative Comp.
99.1% European
Northern European
31.4% British and Irish
23.9% French and German
39.9% Nonspecific Northern European
0.8% Eastern European
Southern European
0.5% Nonspecific Southern European
0.1% Ashkenazi
2.5% Nonspecific European
0.9% East Asian & Native American
0.9% Native American
< 0.1% Unassigned
23andMe Conservative Comp.
97.9% European
Northern European
1.4% British and Irish
53.2% Nonspecific Northern European
0.1% Ashkenazi
43.3% Nonspecific European
0.8% East Asian & Native American
0.8% Native American
< 0.1% Nonspecific East Asian & Native American
1.3% Unassigned
AncestryDNA Updated version
Region Approximate Amount
Europe 99%
Europe West 31%
Scandinavia 26%
Great Britain 15%
Iberian Peninsula 13%
Ireland 10% (includes Scotland and Wales)
Trace Regions 4%
Italy/Greece 3%
Europe East < 1%
West Asia < 1%
Trace Regions < 1%
Caucasus < 1%
AncestryDNA Pre update
Central European 50%
British Isles 42%
Finnish/Volga-Ural 8%
Nat Geo Geno 2.0 Project
Y-DNA YSC234 (subclade of the P58/J1c3 series) mtDNA C1b
Northern European 42%
Mediterranean 38%
Southwest Asian 16%
First Reference Population - German
Second - Tuscan (Italy)
2.5% Neanderthal and 3.7% Denisovan
DNA-me
African 0.20%
American 2.30%
Asian 0.70%
European 96.80%
Updated because the FTDNA information wasn't added.