10 Signs Your Salesforce.com Instance Is In Trouble

1. Duplicate Contacts  - The occasional duplication of data is very common in Salesforce.com. However the majority of duplicates should be coming from user error. I have yet to see a business process that "requires" duplication of contacts.  A properly configured instance of Salesforce.com should rely upon Contact Roles or custom objects to relate one contact with multiple accounts, contacts or cases.
2. Duplicate Accounts - If part of your business process is to duplicate accounts you are most likely making things harder than they have to be. An account by definition should be a physical location (address) and its name. If you have multiple accounts with the same address and name then you should take a step back and ask yourself  why this is occurring and if you are properly using account relationships like the "Parent" field or the "Partner" related list.
3. Losing Data on Lead Conversion - Sounds like a worst case scenario, but you should check to make sure that when you convert a lead into a contact or account that you are not losing any fields in the conversion. If you system is not mapped properly, data can be lost in this step. A properly mapped system will have a corresponding field on the Account or Contact to those seen on the lead.
4. Addiction to Custom Code / Triggers - The occasional trigger or snippet of APEX code can on occasion be unavoidable. However, I cannot emphasize enough that Triggers and Custom Code should be used as a LAST RESORT.  Custom code becomes a maintenance nightmare. The more custom code you have, the harder it is to remember or document what each piece does. So making tweaks to the system becomes a project rather than an afternoon exercise and you have effectively nullified one of the true benefits of Salesforce.com, its ease of modification. The more you can make Standard Salesforce.com work for you, the more you will be thanking yourself in the long run.  
5. Too Many Check Boxes - A common complaint and something that is easily fixed. Look to see if your checkbox could be grouped into different topics and look at using a multi-select picklist to contain all of the values.
6. Everything Is A Required Field - If you make everything required, you are building a system that encourages the user to go back to using pen and paper and spreadsheets to track their data. My rule of thumb has been no more than 5 required fields on a page. Fewer on transactional data such as Activities. Its a matter of priorities and this is a good time to ask what data is really important and what is a "nice to have".
7. No Data On Records - This is the flip side to number 6. For those fields that are essential for running your business or you are planning on using in a report, you should consider making them a required field. Its a balancing act that you know you have gotten just right when both the end users and those running reports are equally miffed.
8. Misuse of Standard Objects - This is a harder one to explain, but I know it when I hear it. Typically it begins with the statement from a client of  "We use <OBJECT NAME> differently then most people.." 8 times out of 10 this one statement is the root cause for why I am being brought in to Consult.  Its important to have a fundamental understanding of what each Salesforce.com object does before you begin to build your system. The more you stray from any objects intended purpose, you more you are inviting a visit from the ghost of unintended consequences.
9. No One Is Using The System- Salesforce.com has no magical powers. It is a tool just like your email or accounting systems. If the system you have built does not provide a compelling reason to login such as, time savings, access to accurate client information, or reporting capabilities, then you should really ask yourself why you invested in a CRM to begin with. 
10. I Can't Run The Reports I Want - Like the old saying, "garbage in, garbage out". To fully utilize Salesforce.com ability to generate reports requires both good data as well as properly structured data. If you can't run the reports that you would like it is the best indication of any that there something is wrong with your instance.