In the interests of giving credit to the resources geneticists find most useful, here are the the numbers of papers citing the most frequently cited links in Nature Genetics papers published in 2006 (volume 38). 108 of 184 papers cited links, totalling 531, with a mean of 2.9 per paper. The paper with the largest number of links was Park with 28.

Databases
9 NCBI Genbank which also has 261 linked nucleotide accessions (no repeat citations yet)
7 GEO with 25 microarray experiments and 5 microarray methods
4 ArrayExpress with 9 microarray experiments (one cited twice)
8 HapMap in Wu Rajewsky Hirschhorn Chakravarti Witt Yoshiura Daly Altshuler
5 dbSNP in Hirschhorn Georges Yoshiura Attie Flint
5 SeattleSNPs in Bhangale Zhang Lee Allikmets Stephens
3 PDB with 3 protein accessions
2 NCBI Trace Archive in Bhangale Stephens
2 RZPD in Timmerman Zeviani
2 GDB in Timmerman Stratakis
2 Cardiogenomics in Disteche Lee

Software
16 UCSC in Frazer Altshuler Wu Hirschhorn Ober Ranum Clark Hildebrandt Attie Harvey Ranum Petit Jackson Crow Chakravarti Radvanyi
6 Ensembl in Timmerman Zeviani Bamshad Mootha Stratakis Petit
5 R in de Laat Radvanyi van Steensel Doebley Weigel
4 ClustalW in Ranum Zeviani Zhang Timmerman
4 Broad in Altshuler Daly Oliver Rosenblatt
4 Haploview in Alarcón-Riquelme Chakravarti Yoshiura Daly
4 BLAST in Johnson Park Fuchs Jackson
3 Stephens lab in Legius Zhang Allikmets
2 CBS DTU in Zeviani Johnson
2 PAUP in Weigel Zhang
2 Clayton lab in Zhang Allikmets

Corporations
5 Affymetrix (you have to double click to come back from this link)
2 Softgenetics
2 Sapio

In the examples above, the citing paper is linked by first listed corresponding author for convenience rather than in accordance with journal policy (which is to cite First Author et. al. or Corresponding Author and colleagues). By following the link, the full authorship can be seen. It is clear that accessions mandated by the journal predominate, but ideally, all publicly deposited resources should be fully cited by authors, and properly logged and counted by the journals.

Thanks to Irina Nudelman for help with analysis, any errors are my own fault - Myles Axton.