depends on your amplicon size and also on your biological question. smaller DNA can be run on PAGE and analysed but for large regions PCR is the normal choice.  could you elaborate on your project?

Abbas, I am doing relationship studies between blueberry wild-types and hybrids through polymorphism. for which I will be using EST-SSR markers. I do not expect more than 1800 bp amplicon.

definitely PAGE. It has much higher resolution. It is common for SSRs' alleles to have single nucleotide difference in length.

PAGE give better resolution

No doubt PAGE gives better resolution but for an amplicon size of 1800 bp, even Agarose electrophoresis will do.

Dear Dhrumit,

Its all depends on your application..is it normal PCR or any others PCR-based methods? as well as your fragment size (amplicon).

If you choose microsatelite PCR or any amplified products below than 100 bp, u can use PAGE for the greatest resolution.

Agarose gel Electrophoresis is easier and readily available but in terms of resolution Polyacrylamide gel Electrophoresis is far better than Agarose.

metaphor agrose

If you need more precision especially for small segmentos page is better. But usually becase is easier everybody use agarose.

Definitely PAGE. I did a similar study looking at small deletion differences between DNA segments of about 1kb and using 8% PA I could resolve differences of 2-10 bp between amplicons.

It's no accident that sequencing gels are polyacrylamide!

It depends on what resolution you want to achieve and for what for? Never mind, you should take other parameters into account before engaging in your separation. For PAGE separation you have to distinguish between native and denaturing conditions. Sequencing gels are denaturing (single stranded). Of course they can give you base pair resolution. The second thing you should bear in mind is that native PAGE is extremely dependent on the sequence. It is well known that some sequences induce DNA curvature which will be translated into lower mobility in native PAGE. Even some bands from commercial marker display this altered mobility pattern. So, you have to be very careful at the time of making a choice and interpreting your separation results.

Definitely PAGE 

but Nusieve agarose at 3% will also give better resolution..

Selection of agarose or PAGE depends on size difference of your PCR products.

Difference more than 10 bp:

Use agarose:

3% agarose gel containing 80% of MetaPhor® Agarose (Cambrex Bio Science Rockland, Inc., Rockland, ME) and 20% of UltraPure™ Agarose (Invitrogen, Carlsbad, CA) (% of agarose depends on length of your fragments).

Difference less than 10 bp:

Use PAGE or ORIGINS Elchrom Scientific electrophoresis (you have to buy Spreadex gels; it is more expensive, but less messy than PAGE).

References for more technical details:

Agarose:

Síma M et al. Genetic control of resistance to Trypanosoma brucei brucei infection in mice. PLoS Negl Trop Dis. 2011 Jun;5(6):e1173. doi: 10.1371/journal.pntd.0001173.

http://www.ncbi.nlm.nih.gov/pubmed/21666791

https://www.researchgate.net/publication/51213078_Genetic_control_of_resistance_to_Trypanosoma_brucei_brucei_infection_in_mice

PAGE:

Krulová M et al. IL-2-induced proliferative response is controlled by loci Cinda1 and Cinda2 on mouse chromosomes 11 and 12: a distinct control of the response induced by different IL-2 concentrations. Genomics. 1997 May 15;42(1):11-5.

http://www.ncbi.nlm.nih.gov/pubmed/9177770

https://www.researchgate.net/publication/14040564_IL-2-induced_proliferative_response_is_controlled_by_loci_Cinda1_and_Cinda2_on_mouse_chromosomes_11_and_12_a_distinct_control_of_the_response_induced_by_different_IL-2_concentrations?ev=prf_pub

ORIGINS Elchrom:

Sohrabi Y et al. Mapping the genes for susceptibility and response to Leishmania tropica in mouse. PLoS Negl Trop Dis. 2013 Jul 11;7(7):e2282. doi: 10.1371/journal.pntd.0002282. Print 2013.

http://www.ncbi.nlm.nih.gov/pubmed/23875032

https://www.researchgate.net/publication/250926206_Mapping_the_Genes_for_Susceptibility_and_Response_to_Leishmania_tropica_in_Mouse?ev=prf_pub

Article Genetic Control of Resistance to Trypanosoma brucei brucei I...

Article IL-2-Induced Proliferative Response Is Controlled by LociCin...

Article Mapping the Genes for Susceptibility and Response to Leishma...

Thank you so much maria

PAGE is better. if size of product is small then go for PAGE otherwise Agarose