Introduction
In November 2011 Yahoo Site Explorer ceased to exist. This free service was quite popular among SEO specialists and web-site owners. They used it to determine link popularity of their websites as well as to study the link building strategy of competitors.
As the Yahoo service was abandoned, the popularity of other backlink analysis services existed at that moment had increased. These were Open Site Explorer, Backlink Watch and Majestic SEO. On the other hand, a handful of alternative services had emerged, including Ahrefs, Web SEO Analytics, Monitor Backlinks and others.
Now there are dozens of paid and free tools for back link research. Choosing a certain practical instrument from such vast variety based on the price/quality ratio seems a difficult task to me. And while one or another SEO blog periodically publishes articles named like “5 Top Backlink Checker Tools for Your Website” or “7 Best Free Online Backlink Checker Tools You Should Know About”, it is always remain unclear, what are those criteria the authors use to determine the best services. 
The list below encompasses all tools to search and analyze backlinks known to me. The list consists of four parts. The first one includes backlink explorers presented in webmaster tools of such search engines as Google, Bing and Yandex. The second part of the list covers online services. The third part lists API you can use in your own applications. The fourth part contains the collection of desktop software. Each part of the list is sorted alphabetically.
Please keep in mind that backlink checking is merely one of functions most paid services offer. So by purchasing monthly subscription you also receive access to other useful SEO tools.
You won’t find qualitative comparison of backlink tools in my list. Such comparison is a subject for in-depth research, though I plan to eventually publish it in the blog. But even those characteristics that are listed below in the brief description of each document can be used to preliminary estimate capabilities of these services. Besides, every tool can be ranked: I encourage you to vote for your favorite tools to help determining the most popular instrument among those listed below.
In the future, I plan to refresh this list by removing abandoned tools and adding new ones. If you are aware of some backlink tools not included in my list yet, please let me know in your comments.
Content
Webmaster Tools
1. Bing Webmaster Tools
2. Bing Webmaster Tools - Link Explorer
3. Google Webmaster Tools
4. Yandex.Webmaster
Online Backlink Checkers
5. Ahrefs Backlinks Report
6. Ahrefs Site Explorer
7. Alexa
8. Backlink Watch
9. Backlinktest.com
10. cognitiveSEO Backlink Checker & Site Explorer
11. European-Business-Connect.de
12. Indexicon - Free Backlink Checker
13. linkbird
14. Linkody
15. Linkody - Backlink Checker
16. LinkPad
17. LinkResearchTools - Backlink Profiler (BLP)
18. LinkResearchTools - Quick Backlinks (QBL) Tool
19. Majestic
20. Monitor Backlinks - Free Backlink Checker SEO Tool
21. MoonSearch
22. Open Site Explorer
23. OpenLinkProfiler
24. RankSignals.com
25. Searchmetrics Suite - Backlink Check & Analysis Tool
26. SEMrush
27. SEOkicks
28. SEOlytics
29. SEOprofiler
30. Sheer Explorer
31. Site Explorer
32. SmallSEOTools.com
33. Web SEO Analytics
34. WebMeUp backlink tool
Backlink Checker API's
35. Ahrefs API
36. Majestic API
37. Mozscape API
38. SEMrush API
39. SEOkicks API
Backlink Checker Software
40. SEO SpyGlass
41. Traffic Travis
Webmaster Tools
1. Bing Webmaster Tools
http://www.bing.com/toolbox/webmaster
3/5 (11 votes)
Access
free
Free version
as many backlinks as they consider appropriate to show
for verified domains only (ie you must be the owner of the domains)
Own web crawler
yes (Bingbot)
2. Bing Webmaster Tools - Link Explorer
http://www.bing.com/toolbox/link-explorer
3.1/5 (12 votes)
Access
free
Free version
as many backlinks as they consider appropriate to show
Own web crawler
yes (Bingbot)
3. Google Webmaster Tools
http://www.google.com/webmasters
3.6/5 (17 votes)
Access
free
Free version
as many backlinks as they consider appropriate to show
for verified domains only (ie you must be the owner of the domains)
Own web crawler
yes (Googlebot)
4. Yandex.Webmaster
http://webmaster.yandex.ru
2.6/5 (8 votes)
Access
free
Free version
as many backlinks as they consider appropriate to show
for verified domains only (ie you must be the owner of the domains)
Own web crawler
yes (YandexBot)
Online Backlink Checkers
5. Ahrefs Backlinks Report
https://ahrefs.com/reports
2.6/5 (16 votes)
Access
free & paid
Free version
up to 500 backlinks per report (for unverified domains)
up to 3 reports per month (for unverified domains)
up to 5,000(?) backlinks per report for verified domains (ie you must be the owner of the domains)
Paid version
$79/month - up to 5,000(?) backlinks per report; up to 100 reports per month
$179/month - up to 15,000(?) backlinks per report; up to 250 reports per month
$499/month - up to 30,000(?) backlinks per report; up to 500 reports per month
Own web crawler
yes (AhrefsBot)
Related API
Ahrefs API
Related online service
Ahrefs Site Explorer
6. Ahrefs Site Explorer
https://ahrefs.com/site-explorer
2.8/5 (22 votes)
Access
free & paid
Free version
up to 10 backlinks per report
only one report per day!
Paid version
$79/month - up to 5,000 backlinks per report
$179/month - up to 15,000 backlinks per report
$499/month - up to 30,000 backlinks per report
Own web crawler
yes (AhrefsBot)
Related API
Ahrefs API
Related online service
Ahrefs Backlinks Report
7. Alexa
http://www.alexa.com/plans
2.2/5 (16 votes)
Access
paid
Paid version
from $9.99/month - as many backlinks as there are in their index
free 30 days trial
Own web crawler
yes (ia_archiver)
8. Backlink Watch
http://backlinkwatch.com
2.5/5 (20 votes)
Access
free
Free version
up to 1,000 backlinks per report
Own web crawler
no
Backlinks providers
information is not available
9. Backlinktest.com
http://www.backlinktest.com
2.3/5 (18 votes)
Access
free
Free version
as many backlinks as there are in their index
Own web crawler
yes (unknown)
Notes
CAPTCHA
10. cognitiveSEO Backlink Checker & Site Explorer
http://explorer.cognitiveseo.com
2.5/5 (13 votes)
Access
free & paid
Free version
up to 25 backlinks per report
Paid version
$99/month - 10,000 backlinks per report
$199/month - 15,000 backlinks per report
$499/month - 50,000 backlinks per report
$999/month - as many backlinks as there are in their index
free 14 days trial
Own web crawler
yes - ? (James BOT – WebCrawler)
Backlinks providers
Ahrefs API
Majestic API
Mozscape API
SEOkicks API
11. European-Business-Connect.de
http://www.european-business-connect.de/backlinkchecker.php
2.6/5 (9 votes)
Access
free
Free version
up to 2,500 backlinks per report
Own web crawler
yes - ? (unknown)
Notes
the website is in German only
CAPTCHA
12. Indexicon - Free Backlink Checker
http://www.indexicon.com/free-backlink-checker
2/5 (10 votes)
Access
free
Free version
up to 16,000 backlinks per report; one report per day
Own web crawler
no
Backlinks provider
LinkResearchTools - Quick Backlinks (QBL) Tool
Notes
reports in CSV-format come by email within a few hours
13. linkbird
https://www.linkbird.com
2.4/5 (7 votes)
Access
paid
Paid version
from €79.90/month
free 14 days trial
Own web crawler
no
Backlinks provider
SEOkicks API
14. Linkody
http://www.linkody.com
2.6/5 (11 votes)
Access
paid
Paid version
several dozens/hundreds of discovered backlinks per monitored domain (limitations are not specified)
$9.90/month - up to 3 monitored domains
$29.90/month - up to 20 monitored domains
$69.90/month - up to 100 monitored domains
free 30 days trial (up to 2 monitored domains; no CSV export)
Own web crawler
no
Backlinks providers
information is not available
15. Linkody - Backlink Checker
http://www.linkody.com/en/seo-tools/free-backlink-checker
2.8/5 (6 votes)
Access
free
Free version
a few top backlinks per domain; up to 2 domains per week
Own web crawler
no
Backlinks providers
information is not available
Notes
CAPTCHA
16. LinkPad
http://www.linkpad.ru
2.8/5 (9 votes)
Access
free
Free version
up to 5,000 backlinks per report
Own web crawler
yes (LinkpadBot)
Notes
the website is in Russian only
17. LinkResearchTools - Backlink Profiler (BLP)
http://www.linkresearchtools.com/tools/blp
3.3/5 (7 votes)
Access
paid
Paid version
€99/month - up to 12,500 backlinks per report; up to 10 reports per month
€299/month - up to 20,000 backlinks per report; up to 100 reports per month
€469/month - up to 40,000 backlinks per report; up to 250 reports per month
€1,299/month - up to 50,000 backlinks per report; up to 1,250 reports per month
Own web crawler
yes (unknown)
18. LinkResearchTools - Quick Backlinks (QBL) Tool
http://www.linkresearchtools.com/tools/qbl
3/5 (8 votes)
Access
paid
Paid version
€99/month - up to 5,000 backlinks per report; up to 100 reports per month
€299/month - up to 8,000 backlinks per report; up to 200 reports per month
€469/month - up to 16,000 backlinks per report; up to 500 reports per month
€1,299/month - up to 30,000 backlinks per report; up to 2,500 reports per month
free 7 days trial (up to 16,000 backlinks per report; up to 10 reports)
Own web crawler
yes (unknown)
19. Majestic
https://majestic.com
3.1/5 (14 votes)
Access
free & paid
Free version
up to 5,000 backlinks per report
for verified domains only (ie you must be the owner of the domains)
Paid version
$78.99/month - up to 5,000 backlinks per report, up to 5,000,000 downloadable backlinks/month
$169.99/month - up to 15,000 backlinks per report; up to 25,000,000 downloadable backlinks/month
$399.99/month - up to 30,000 backlinks per report; up to 100,000,000 downloadable backlinks/month
$799.98/month - up to 40,000 backlinks per report; up to 300,000,000 downloadable backlinks/month
$1,599.96/month - up to 50,000 backlinks per report; up to 1,000,000,000 downloadable backlinks/month
Own web crawler
yes (MJ12bot)
Related API
Majestic API
20. Monitor Backlinks - Free Backlink Checker SEO Tool
http://monitorbacklinks.com/seo-tools/free-backlink-checker
2.4/5 (11 votes)
Access
free
Free version
up to 300 backlinks per report
up to 2 reports per week
Own web crawler
no
Backlinks provider
Ahrefs API
Notes
a free or paid account is required
CAPTCHA
21. MoonSearch
http://moonsearch.com
2.2/5 (9 votes)
Access
free
Free version
as many backlinks as there are in their index
Own web crawler
yes (unknown)
22. Open Site Explorer
https://moz.com/researchtools/ose
2.3/5 (15 votes)
Access
free & paid
Free version
up to 200 backlinks per report
limited functionality
Paid version
from $99/month - up to 10,000 backlinks per report
free 30 days trial
Own web crawler
yes (rogerbot)
23. OpenLinkProfiler
http://www.openlinkprofiler.org
3.2/5 (19 votes)
Access
free
Free version
shows online up to 200,000 backlinks per report
up to 1,000 backlinks can be exported in csv-format
Own web crawler
yes (spbot)
Related online service
SEOprofiler
24. RankSignals.com
http://www.ranksignals.com
2.3/5 (9 votes)
Access
free
Free version
as many backlinks as there are in their index
Own web crawler
yes (unknown)
25. Searchmetrics Suite - Backlink Check & Analysis Tool
http://suite.searchmetrics.com/en/research/links/backlink-analysis
2.2/5 (13 votes)
Access
free & paid
Free version
up to 10 backlinks per report without registration
up to 500 backlinks per report with a free account
Paid version
from $69/month - as many backlinks as there are in their index
Own web crawler
yes (SearchmetricsBot)
26. SEMrush
http://www.semrush.com
3.6/5 (20 votes)
Access
free & paid
Free version
up to 10 backlinks per report
Paid version
$69.95/month - up to 10,000 backlinks per report
$149.95/month - up to 30,000 backlinks per report
$499/month - up to 100,000 backlinks per report
Own web crawler
yes (SemrushBot)
Related API
SEMrush API
27. SEOkicks
<