I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what stand alone packages would you now recommend?
I would strongly recommend benchling https://benchling.com
This is an awesome web based tool for cloning, primer design, multiple sequence alignments and everything else you are used to doing with the other tools. It is very user friendly, and most importantly you can share designs with your collaborators. Also, the graphics are very beautiful. I recently started using it and I am really impressed with the technical support they offer: you can chat with them and they would reply within minutes. Also, if there is a feature you would like to have implemented they would definitely consider it. Benchling is free, open source and you might be even able to code up some features yourself.
I personally use more frequently Geneious for most of the basic every-day manipulations (my university bought a license), but I would recommend Ugene: it's free, open-source, cross-platform and supports batching and scenarios.
I would recommend Galaxy. https://usegalaxy.org/ The system does include primer design, sequence alignments and covers many common bioinformatics tasks.
For primer design you can use the Gene Designer: https://www.dna20.com/resources/genedesigner
For sequence alignment you can use BLAST (from the NCBI, also downloadable as a standalone tool)
Of course there are better options that might be more specific for your situation.
If it's not loo late to contribute, CLC workbench is nice too (http://www.clcbio.com/products/clc-main-workbench/). I only use the free version (http://www.clcbio.com/products/clc-sequence-viewer/) but its very user friendly in terms of the features I have worked with.
Geneious is probably the strongest standalone package, but real bionformaticians rarely deal with GUI driven programs.