Family Search is an index of baptisms and marriages from (mainly) Church of England registers. Whilst far from complete it can make a very good starting point. A list of what parishes are covered by Family Search can be found on the rootsweb web site. The Manchester Room@City Library has the microfiche version for the British Isles.
The Lancashire Online Parish Clerks project site aims to extract and preserve the records from the various parishes and to provide online access to that data, free of charge. Transcripts of various parish registers are available on this web site.
The Manchester and Lancashire Family History Society have started to create an index to persons named in the Manchester Roman Catholic registers. This index is available on their web site.
BMDRegisters is a searchable on-line service of early non-conformist birth, marriage and death registers held at the National Archives.
The Manchester Room@City library possess a CDROM index of burials at Manchester Cathedral 1573-1868.