The following comparison is based on the article http://timesofindia.indiatimes.com/india/Aruna-Roys-bill-seeks-to-fine-tune-clauses-in-Annas-Jan-Lokpal/articleshow/9700516.cms. I will add more to this as I read the bills in more detail and/or come across other comparisons of all three bills.

Government’s bill Jan Lokpal Bill (By Anna’s team) Lokpal – NCPRI proposal My Comments
Limits the bill to Lokpal at the Centre. The same law should also establish Lok Ayuktas in the states. The same law should also establish Lok Ayuktas in the states. Many states already have Lok ayuktas or equivalent. Odisha and Karnataka come to mind. Also, if it is extended to the states, the viewpoints of the  states need to be taken. That will take time.
  All the levels of bureaucracy should come under Lokpal CVC should be strengthened to deal with lower bureaucracy.  I prefer the NCPRI proposal as it will keep the Lokpal part focused and less bureaucratic.
Prime Minister is exempted from Lokpal’s ambit. Prime Minister should not be exempted from Lokpal’s ambit. Prime Minister should not be exempted from Lokpal’s ambit. But, there should be no investigation without the Supreme Court’s clearance and that the Cabinet’s collective responsibility should not expose him to vicarious liability.  I like the NCPRI proposal.
Chairperson has to be a judge. Need not be a judge. Need not be a judge. Judges have a record which one can scrutinize to find out if he/she has been fair, if he she has been following the constitution, if he/she has been ignoring the law to appease popular sentiments, etc.
Nine-member selection committee   Three member selection committee: Prime Minister, leader of opposition in the Lok Sabha and a SC judge. A 10-member search committee, which will short-list candidates, should consist equally of retired state functionaries and civil society representatives.  I think the US methods of confirming a Supreme Court Justice should be added. I.e., After the selection the Chairperson should be confirmed by a majority of the MPs (perhaps in a secret ballot) without any whips. The confirmation process should include questioning by the MPs, as is done in case of US supreme court judge confirmations. 
Allegations against the Lokpal should not be probed by the SC without a reference by the President. No such condition. No such condition.   
Lokpal to deal with complaints against its officials. Inquiry should instead be held by an ombudsman appointed by an independent committee. Inquiry should instead be held by an ombudsman appointed by an independent committee.   
Exempting MPs from Lokpal’s remit for their conduct in Parliament No such exemption. NCPRI’s view is that a constitutional amendment is required to remove the immunity enjoyed by MPs. It calls for an undertaking from the government that it would make such an amendment within a year.  
Extraordinary safeguard in the official bill requiring Lokpal to give a hearing to the accused public servant before registering an FIR against him. Does not agree. Does not agree. Here, I prefer the government’s version. There are a lot of honest government officers and lawmakers. If they are accused, they should be provided a hearing, Otherwise people will just stop making decisions or taking initiatives as that would be the best way to avoid hassles.
A complainant found to have filed a frivolous case be liable to imprisonment for at least two years.   A monetary penalty not exceeding Rs 1 lakh. Here I am more in the side of the government. Frivolous cases can put everything to a halt and needs to be strongly dissuaded. These days Rs. 1 lakh penalty is nothing. Unless people are sure they should not be making complaints to the Lokpal. There are other means (go to press, file PIL, etc.) where the penalty is much less.
       

In http://164.100.47.5/newcommittee/press_release/press/Committee%20on%20Personnel,%20PublicGrievances,%20Law%20and%20Justice/PR%20-%20LB,%202011.pdf the parliament standing committee on this bill asks for a feedback memorandum. Following is a quote from that:

Those desirous of submitting memoranda to the Committee may send two copies thereof, neatly typed in double space (either in English or Hindi) to Shri K.P. Singh, Director, Rajya Sabha Secretariat, 201, Second Floor, Parliament House Annexe, New Delhi-110001 (Tel: 23034201, Fax: 23016784, E-mail: kpsingh@sansad.nic.in and rs-cpers@sansad.nic.in) within fifteen days of publication of this advertisement. Those who are willing to appear before the Committee for oral evidence besides submitting the memorandum may so indicate.

The Date of Publication of the above notice is 20th August, 2011 and the Last date for Submitting a Memorandum is 3rd September, 2011.

Following is a comparison of the Lokpal Bill and JanLokpal Bill by Hindustan Times. The part I agree with is annotated in red.