The majority of historical church records for London and Middlesex are held by four repositories:
London Metropolitan Archives hold records for most Anglican parishes in Middlesex, though the registers for a few ancient parishes have not been deposited, and some are elsewhere. They also have a wide range of 19th and 20th century non-conformist records. All registers held at LMA are listed on the London Generations Database.
Guildhall Library holds records for most Anglican parishes in the City of London, and some of the Middlesex parishes that adjoin the City.
The City of Westminster Archives Centre holds records for most Anglican parishes in the former Metropolitan Borough of Westminster (corresponding to the southern part of the current City of Westminster), though some from this area are not deposited and others are at LMA.
The National Archives hold registers from non-conformist and non-parochial Anglican churches and chapels surrendered to the Non-parochial Registers Commissions of 1837 and 1857.
There are other record offices which hold church records relating to individual parishes in the City of London and Middlesex. Where we know about them they are listed on the appropriate parish page.
For non-conformist records, Dr Williams Library has some resources for the study of the history of various denominations, but does not hold Dr Williams Libary Registers which are at the National Archives.
A search on the Society of Genealogists library catalogue for the subject "LONDON/MIDDLESEX - REGISTERS" (use exactly that search term including spaces and symbols), gives an indication of some of the records that are available. Copies of the registers mentioned are likely to be available at other locations as well.
Marriage licences at Guildhall Library - their leaflet is "a brief introduction to searching for records relating to the issue of marriage licences, with particular reference to those held by the Manuscripts Section of Guildhall Library and elsewhere concerning the City of London and former county of Middlesex."
"A Guide to Middlesex Parish Documents (including Poor Law Records)" by Cliff Webb, published by West Surrey FHS, (3rd edn 1998) is a helpful list for parishes founded before about 1830.
Harleian Society Parish Register Publications: The Harleian Society published almost 90 volumes of parish registers between 1877 and 1979, as the Register Series, with one in the New Series. Most of them relate to the City of London and the adjoining parts of Middlesex. The volumes are usually full transcriptions, omitting common phrases, and each contains an index.. For burial records for the period 1754-1812, John Hanson has reported an error rate of up to 10%, including mis-transcriptions and missing entries, and presumably that the error rate is similar throughout.
The British Vital Records Index (BVRI) continues the IGI in CD format, and indexes births, baptisms and marriages. The Genoot website provides lists of the registers covered for births and christenings and marriages.
The bmdregisters.co.uk website (pay-per-view) indexes National Archives classes RG4 covering non-parochial registers, and RG5 covering the non-conformist registry of Dr Williams' Library and the Wesleyan Methodist Registry. They provide a brief overview of the content. Searching the National Archives Catalogue for these classes may give a better idea of the coverage. Some of these registers are also covered by the IGI and BVRI.
FreeREG aims "to provide free Internet searches of baptism, marriage, and burial records, that have been transcribed from parish and non-conformist registers." Their coverage of London and Middlesex is limited at the moment, but they provide pages listing the City of London and Middlesex registers covered. More volunteer transcribers are needed.
Arthur Hopkins has transcribed the Quaker London & Middlesex Quarterly Meeting records for selected surnames, births 1654-1719, marriages 1658-1775, and burials 1670-1719. They are published on his website.
Pallot's Baptism Index once included 12 million entries, but it was mostly destroyed in the Second World War, so that only 200,000 entries remain. It covered 1780-1840 for at least 22 London and Middlesex parishes, but is obviously now incomplete. However as compilation of the Pallot indexes started in 1818 it is possible that it contains entries from registers now destroyed. The card index is owned and held at the Institute of Heraldic and Genealogical Studies, who sell copies on CD, and it is available online via Ancestry.
Dockland Ancestors Ltd offer indexes to baptisms for a number of East End and Docklands parishes, which are otherwise poorly covered by indexes. They also sell these indexes on CD.
Pallot's Marriage Index for 1780-1837 has excellent coverage of the City of London and good coverage of Middlesex. Like the Pallot's Baptism Index it was started in 1818 and contains entries from registers now destroyed, but this index survives intact. The card index is owned and held at the Institute of Heraldic and Genealogical Studies, who sell copies on CD, and it is available online via Ancestry. The original handwritten slips are hard to read and thus many errors have crept into the electronic version.
Boyd's Marriage Index was compiled by Percival Boyd between 1925 and 1955, usually using printed and transcribed sources. It covers marriages in most of the parishes of Middlesex and the City of London for varying periods. The original index is at the Society of Genealogists, and an online version is available on FindMyPast which previously had a useful explanation of the structure of the index. Listings of the parishes covered were formerly on the Origins website, and may now be found on the Internet Archive for London and Middlesex. Microform copies of the index can be found in many local repositories, including the Guildhall Library. The LDS Family History Library has microfilm and microfiche versions. Search their catalogue for the title "Boyd's marriage index" to locate them.
Cliff Webb has started a project to produce a supplement to Boyd's index for London and Middlesex parishes not covered in it; this will also include Jewish, Roman Catholic and Huguenot marriages. The work is ongoing but thousands of records are already available on Origins Network, with a list of the parishes and periods covered. The announcement of this project in the Genealogists' Magazine also promised hardcopy at the Society of Genealogists and the Guildhall Library.
Crisp's London Marriage Licences Index covers marriage licences from more than a dozen large London parishes from the mid-1700s to 1837. It may be searched by surname for free on the Achievements website, and an abstract of the content is available for a fee.
Marriage licences issued by the Archbishop of Canterbury's Vicar-General or the Faculty Office at Doctor's Commons, could be for anywhere in the Archdiocese of Canterbury, but these licence were particularly used by London and Middlesex couples. There are indexes to the Vicar-General records 1694-1850 and the Faculty Office records 1701-1850 at the Society of Genealogists, and an online version of them is available on FindMyPast with a useful description of the indexes and records.
British Record Society volume 62 (1597-1648) and volume 66 (1660-1700) give chronological calendars of the names of parties, but contain many errors.
Records of selected licences from 1521 to 1869 (very few after 1648) are abstracted in London marriage licences, 1521-1869 edited by Joseph Foster (1887) based on extracts by Joseph Lemuel Chester.
Selected licences from 1520 to 1828 (complete to 1597, 'the most important .. down to about 1700', very few after that date) are abstracted in Harleian Society volume 25 (1520-1610) and volume 26 (1611-1828), edited by George Armytage and also based on extracts by Joseph Lemuel Chester.
Boyd's London Burial Index covers 243,000 male burials in London. It is available at the Society of Genealogists or online at FindMyPast, which used to provide a description of the index and a list of parishes covered. Boyd himself described this index as "a 'lucky dip' if you find what you want, well & good; if you don't, you have searched nothing", because it is neither systematic nor comprehensive.
Hanson & Stevens' index aims to cover the City parishes not included in Webb's index, and to extend it back to 1754. It is available from findmypast.co.uk, co-searchable with Webb's index. It currently covers all the remaining City of London parishes, and a number of the adjoining Middlesex and Surrey parishes for 1813-1854. Work is ongoing to index the period 1754-1812. John Hanson has provided a very detailed account of these indexes.