First of all do opening balance testing, check whether there are any deviations from the balances as per last audited balance sheet and opening figures of the year being audited.
Then, check whether entries recorded are in accordance with the accounting principles.
Creation of Provisions.
Prior period expenses (By going through Invoices)
Proper calculation of Prepaid expenses.
Proper capitalisation of assets and calculation of deprecaition.
Various statutory dues like Service tax, TDS, VAT/CST, Excise & Custom duties, PF, Professional tax are paid within the due date and accounted properly in books of accounts. Accounting in case of penalty and interest charged by the govt. authorities.
For TDS, Party ledgers should be scrutinized 100%.
Check applicability of various accounting standards and their implications on the entity of which you are doing ledger scrutiny.
Check from the view point of Section 40 A 3, 40 A 2b, 269 SS, 269 T, 2(22)(e), 43 B of income tax act. Section 372 A, 295, 205 of companies act.
There could be many more points but these are the main points which should not be ignored.