Your question says your snps are in the non coding region but also says you are interested in snps in splice sites which are in genes. So i'll just assume most of your snps aren't in genes but some could be.
If you look at gen2phen.org you will see a link called functional classifcation which gives about 10 categories by which SNPs can be annotated and lists tools for each one. This classification is based on a pipeline called 'pathogenic or not pipeline' whose url i can't remember.
The broadest SNP annotation is called a gene annotation whicn annotates snps with respect to genes and classifies them as things like intronic/upstream/downstream/intergenic/3prime_utr, 5'_utr, splice site and for exonic snps stop lost, stop gained, missense etc. I know you said your snps were in the non-coding region of the genome but you might want to know genes/transcripts they are in close proximity to and these tools will tell you that.
There are then tools that look at missense mutations to see if this could have a pathogenic effect on protein structure (polyphen and snp). If you only have intergenic snps you won't be that interested in this. I just felt it would be remiss not to mention these tools as these are the ones that dominate the literature.
You will be most interested in tools which classify snps with respect to regulatory regions such as transcription factor binding sites, promoters, RNA genes. There are tonnes of these and you will see links on the page I gave. if your snp is in a rna gene, for example, tools can tell you the effect of the snp on the rna structure. I don't know whether you are aware that some rna molecules regulate gene expression and may not be able to bind to their target site if their structure is compromised (you said your biology was weak - i hope that's not patronising). For splice sites there are tools to tell you if the snp will produce aberrant splicing.
The best tool that i have seen recently is ANNOVAR. This will let you find annotate public and novel SNPs from any species with respect to any genomic feature for which a GFF3 or VCF file exists. So you can download UCSC genome tracks for known genes, transcription factor binding sites, RNA genes etc etc and get your SNPs annotation with respect to these tracks. I've never used it but apparently its very quick and can annotate 5 million snps in 5 mins. This also has the sequence conservation information you mention in the question
Another tool is the ensembl variation API and a snp effect predictor script from ensembl which will tell you the general consequences of a SNP (the ones listed above) for public/novel snps from any species. I think annovar lets you annotate with respect to ensembl genes anyhow so you might be best with just annovar
SNPNexus is also a 'general' consequence tool.
Papers for all of these tools are available on the gen2phen website