To my limited knowledge, a rough comparison can be done in terms of impact factor (indexed journals) and submissions to publication time consumption ( journal insights) etc. But a precise comparion of quality of works depends on the particular paper itself and not exactly on journal, because low impact journals also publishes good works, although the reverse may not be true. This is my opinion, I am also interested to know answers of RG experts.
The following points may be considered for comparison:
Readership,
Scientific status or impression among the domain experts,
Impact factor (SCI journals) and its trend (decreasing or increasing),
Length of time from submission to publication,
Possibility of acceptance,
Service provided during reviewing process,
Responsiveness of the publisher to any query,
Free of charge or processing fee requires,
Copyright agreement,
Open source facility or not etc.
Chitra Devi has mentioned some points. Above information can be obtained from the websites/publishers, reviews or experience of seniors or fellow colleagues.
First, the Scimago online enables you to make a nice comparison between two journals, but if you need further data, then you could access the publisher's site of these journal, and compare the information provided there. A third way is to follow the journals' papers and observe the journal's trends in the choice of articles for publication, in the subjects covered, countries, languages etc. There is a database that gives you more information on journals, entitled "Ulrich'sGlobal guide to periodical literature", this database provides meta-information on journals, such as circulation counts, when the journal started appearing, frequency of publication, is it still active, and more.
I agree with Asit Kumar and Avishag Gordon. The scimago online database and the online 'directory of open access journals' would be sufficient for comparing the performance indicators of two or more journals .